From unknown Sat Sep 13 08:57:06 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46869] [PATCH] gnu: hmmer: Update to 3.3.2. Resent-From: Tim Howes Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 02 Mar 2021 05:46:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 46869 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46869@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.161466390118778 (code B ref -1); Tue, 02 Mar 2021 05:46:01 +0000 Received: (at submit) by debbugs.gnu.org; 2 Mar 2021 05:45:01 +0000 Received: from localhost ([127.0.0.1]:51400 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGxq5-0004sB-2J for submit@debbugs.gnu.org; Tue, 02 Mar 2021 00:45:01 -0500 Received: from lists.gnu.org ([209.51.188.17]:40266) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGxq2-0004s3-Ou for submit@debbugs.gnu.org; Tue, 02 Mar 2021 00:44:55 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:37456) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lGxq2-0007mU-F4 for guix-patches@gnu.org; Tue, 02 Mar 2021 00:44:54 -0500 Received: from lavabit.com ([38.147.122.66]:9004) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lGxq0-0003RZ-Ly for guix-patches@gnu.org; Tue, 02 Mar 2021 00:44:54 -0500 Received: from localhost.localdomain (158-51-81-84.pool.common.net [158.51.81.84]) by lavabit.com with ESMTP id G8Y2JH0VBUKQ for ; Mon, 01 Mar 2021 23:44:50 -0600 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=lavabit.com; s=bazinga; t=1614663890; bh=HzsakU82fFWMng9kCGaKYusCdcfXqhIYMO/7O8Y2F+M=; h=From:To:Subject:Date:Message-Id:X-Mailer:MIME-Version: Content-Type:Content-Transfer-Encoding; b=MKZYy7pFg+bZWl/jLESfNaUOBTCaPufG3NFSVBKlWQURmT+S4qHmOEk6dG37I7Z2B osKwwP2kqtETXwWAQzqvemfVJYerRwD6uKzXFS9eyJMzU/aOdg//uLD8J/uR4ATorB HmvnswrYlzOpYo3WUUCjit4ZJKHKRwoRJV5S3Qw14hQja5Si6/VNqEEXl0C3CzW/ru XyQ9GpON0jBjOsgXvoVmGvzPJ7MwB1mEvTAPN8KwJkucG3NktJjOBrScFISrXk5joH i2FCAiSTguUgBDJTZnrWMcGe8s7J6BXnqfHD8tl1R2t7iKmKMLdyQQdsU268pwWWgU 173W+z1iqnyyg== From: Tim Howes Date: Mon, 1 Mar 2021 21:44:40 -0800 Message-Id: <20210302054440.41523-1-timhowes@lavabit.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=38.147.122.66; envelope-from=timhowes@lavabit.com; helo=lavabit.com 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, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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: -0.1 (/) * gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 42476a4b2f..48dfe0287e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 Pierre Langlois ;;; Copyright © 2020 Bonface Munyoki Kilyungi +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -3874,7 +3875,7 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (define-public hmmer (package (name "hmmer") - (version "3.2.1") + (version "3.3.2") (source (origin (method url-fetch) @@ -3882,9 +3883,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz")) (sha256 (base32 - "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5")))) + "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl))) + (native-inputs `(("perl" ,perl) + ("python" ,python))) ; for tests (home-page "http://hmmer.org/") (synopsis "Biosequence analysis using profile hidden Markov models") (description -- 2.30.1 From unknown Sat Sep 13 08:57:06 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Tim Howes Subject: bug#46869: closed (Re: [bug#46869] [PATCH] gnu: hmmer: Update to 3.3.2.) Message-ID: References: <20210302054440.41523-1-timhowes@lavabit.com> X-Gnu-PR-Message: they-closed 46869 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 46869@debbugs.gnu.org Date: Wed, 03 Mar 2021 08:15:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1614759301-25762-1" This is a multi-part message in MIME format... ------------=_1614759301-25762-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #46869: [PATCH] gnu: hmmer: Update to 3.3.2. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 46869@debbugs.gnu.org. --=20 46869: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D46869 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1614759301-25762-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 46869-done) by debbugs.gnu.org; 3 Mar 2021 08:14:21 +0000 Received: from localhost ([127.0.0.1]:55081 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHMeD-0006gT-GG for submit@debbugs.gnu.org; Wed, 03 Mar 2021 03:14:21 -0500 Received: from flashner.co.il ([178.62.234.194]:52248) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHMeA-0006gF-Lx for 46869-done@debbugs.gnu.org; Wed, 03 Mar 2021 03:14:20 -0500 Received: from localhost (unknown [31.210.181.184]) by flashner.co.il (Postfix) with ESMTPSA id BB00240221; Wed, 3 Mar 2021 08:14:12 +0000 (UTC) Date: Wed, 3 Mar 2021 10:12:26 +0200 From: Efraim Flashner To: Tim Howes Subject: Re: [bug#46869] [PATCH] gnu: hmmer: Update to 3.3.2. Message-ID: References: <20210302054440.41523-1-timhowes@lavabit.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="x78yo57wCzHMfeGY" Content-Disposition: inline In-Reply-To: <20210302054440.41523-1-timhowes@lavabit.com> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 46869-done Cc: 46869-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: -1.0 (-) --x78yo57wCzHMfeGY Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Thanks! Patch pushed. --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --x78yo57wCzHMfeGY Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmA/ROkACgkQQarn3Mo9 g1EhlQ/9GTPrEXDNIEPRoKPXuvOahKVE+kh2r5XXpVksImgZmAN8USU/5L+9FNRg n/cLfraAoo+SFo2W/j8HXaT7PrTYUcTJGVd7YtmWDzBFSlIhYNy8nJkmMeZj3L7e JPtLME/MRy98yp9/muZdpWLApgoDrsWiVtSF5JwjaWhrMy3i3lZBc4YarTFIissk pu7gw/MbLBYA1TaCWqeePHltNBVHMgFArSa/mdo3dVduSDnTIqB2QCPG5tCdD3DA /A90QMM3uRkTp2/MatH2KmwpP9YYb7QWHGXyZgZjf0UFcS7yeHMDv69+iG9lvQoO DX03cMnKvHuVUMRqse8B6bex1J+zPuYT2K2d8M4GLMe0G4+IgHrWDYSzdnaKABbp W+CoeaqC9lPJHsr818EaDi+f4CQRki7EwdP8BfFleTV/XBArJxa1zEy+n4Hsshwl zvYH25uizFW+0eZibYGflIbmWAnzxqque0AzeY4HukvyHGQhCbHOnSKtylUAik2/ 3Rb8rA2pVCqfl4TrSj/JxBMnfDipr3KEDc7w8ElNl4lmrcFdLXFIpJx+U76sKYYs GOx2pAxORPsbvlaRFqokit8xHG7MQo3iPZEC5RJT2wWRiPftpg9luDI9uZbWmygT SD4HfjRHazDmdngw6r22wmIa4rtqbeUyLeqE6q3qP8wPdhRxmzU= =7zfx -----END PGP SIGNATURE----- --x78yo57wCzHMfeGY-- ------------=_1614759301-25762-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 2 Mar 2021 05:45:01 +0000 Received: from localhost ([127.0.0.1]:51400 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGxq5-0004sB-2J for submit@debbugs.gnu.org; Tue, 02 Mar 2021 00:45:01 -0500 Received: from lists.gnu.org ([209.51.188.17]:40266) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lGxq2-0004s3-Ou for submit@debbugs.gnu.org; Tue, 02 Mar 2021 00:44:55 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:37456) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lGxq2-0007mU-F4 for guix-patches@gnu.org; Tue, 02 Mar 2021 00:44:54 -0500 Received: from lavabit.com ([38.147.122.66]:9004) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lGxq0-0003RZ-Ly for guix-patches@gnu.org; Tue, 02 Mar 2021 00:44:54 -0500 Received: from localhost.localdomain (158-51-81-84.pool.common.net [158.51.81.84]) by lavabit.com with ESMTP id G8Y2JH0VBUKQ for ; Mon, 01 Mar 2021 23:44:50 -0600 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=lavabit.com; s=bazinga; t=1614663890; bh=HzsakU82fFWMng9kCGaKYusCdcfXqhIYMO/7O8Y2F+M=; h=From:To:Subject:Date:Message-Id:X-Mailer:MIME-Version: Content-Type:Content-Transfer-Encoding; b=MKZYy7pFg+bZWl/jLESfNaUOBTCaPufG3NFSVBKlWQURmT+S4qHmOEk6dG37I7Z2B osKwwP2kqtETXwWAQzqvemfVJYerRwD6uKzXFS9eyJMzU/aOdg//uLD8J/uR4ATorB HmvnswrYlzOpYo3WUUCjit4ZJKHKRwoRJV5S3Qw14hQja5Si6/VNqEEXl0C3CzW/ru XyQ9GpON0jBjOsgXvoVmGvzPJ7MwB1mEvTAPN8KwJkucG3NktJjOBrScFISrXk5joH i2FCAiSTguUgBDJTZnrWMcGe8s7J6BXnqfHD8tl1R2t7iKmKMLdyQQdsU268pwWWgU 173W+z1iqnyyg== From: Tim Howes To: guix-patches@gnu.org Subject: [PATCH] gnu: hmmer: Update to 3.3.2. Date: Mon, 1 Mar 2021 21:44:40 -0800 Message-Id: <20210302054440.41523-1-timhowes@lavabit.com> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=38.147.122.66; envelope-from=timhowes@lavabit.com; helo=lavabit.com 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, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) 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: -0.1 (/) * gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 42476a4b2f..48dfe0287e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 Pierre Langlois ;;; Copyright © 2020 Bonface Munyoki Kilyungi +;;; Copyright © 2021 Tim Howes ;;; ;;; This file is part of GNU Guix. ;;; @@ -3874,7 +3875,7 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (define-public hmmer (package (name "hmmer") - (version "3.2.1") + (version "3.3.2") (source (origin (method url-fetch) @@ -3882,9 +3883,10 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") "http://eddylab.org/software/hmmer/hmmer-" version ".tar.gz")) (sha256 (base32 - "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5")))) + "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj")))) (build-system gnu-build-system) - (native-inputs `(("perl" ,perl))) + (native-inputs `(("perl" ,perl) + ("python" ,python))) ; for tests (home-page "http://hmmer.org/") (synopsis "Biosequence analysis using profile hidden Markov models") (description -- 2.30.1 ------------=_1614759301-25762-1--