From unknown Mon Aug 18 14:16:23 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#75727 <75727@debbugs.gnu.org> To: bug#75727 <75727@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add r-sigfit. Reply-To: bug#75727 <75727@debbugs.gnu.org> Date: Mon, 18 Aug 2025 21:16:23 +0000 retitle 75727 [PATCH] gnu: Add r-sigfit. reassign 75727 guix-patches submitter 75727 Alexis Simon severity 75727 normal tag 75727 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 21 07:25:06 2025 Received: (at submit) by debbugs.gnu.org; 21 Jan 2025 12:25:06 +0000 Received: from localhost ([127.0.0.1]:53512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1taDJZ-00088w-Ug for submit@debbugs.gnu.org; Tue, 21 Jan 2025 07:25:06 -0500 Received: from lists.gnu.org ([2001:470:142::17]:58436) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1taDJX-00086P-1f for submit@debbugs.gnu.org; Tue, 21 Jan 2025 07:25:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1taDJO-0000Dk-Ey for guix-patches@gnu.org; Tue, 21 Jan 2025 07:24:54 -0500 Received: from mailtransmit05.runbox.com ([2a0c:5a00:149::26]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1taDJJ-0000vq-DP for guix-patches@gnu.org; Tue, 21 Jan 2025 07:24:54 -0500 Received: from mailtransmit02.runbox ([10.9.9.162] helo=aibo.runbox.com) by mailtransmit05.runbox.com with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256 (Exim 4.93) (envelope-from ) id 1taDJA-000mil-SS for guix-patches@gnu.org; Tue, 21 Jan 2025 13:24:40 +0100 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=runbox.com; s=selector2; h=Content-Transfer-Encoding:MIME-Version:Message-ID:Date: Subject:Cc:To:From; bh=vIcv92f45omMnYAnF/SRupTlnmkFDHALkBcAc0WodoM=; b=Ayjixy uTzU0F0x2TZnviX2+tHfO8GQ1Z1ua1Az2WbB4JcjskN1iL6oyDlHInwtzB9NlwlMrJ0Ru17JAjMAc Ja54qjt3zOUNilr8gtSqM5NRbq0N2wnqw9zw8KkG0bO/RKL19KARvOOiKFAc60hBvegQZyXRWcqkb stYlB3+C9BS4fQ2tspR1MpVOHBbr+ZJHyGFdapgX2ieZ+/VRMOQ8FywjFBxcDL16gPQcM1G+Xvixf Vt5lOPD3F0+cj66wf96uwj2giz8LwurZiaoc6h/avVs5oOcXM0Qeacx+DG9lbmvoZP57gdG9w+nSW x09RV/zBqrP9rPfZ4ny+HM4lcBMQ==; Received: from [10.9.9.74] (helo=submission03.runbox) by mailtransmit02.runbox with esmtp (Exim 4.86_2) (envelope-from ) id 1taDJA-0001Vd-H1 for guix-patches@gnu.org; Tue, 21 Jan 2025 13:24:40 +0100 Received: by submission03.runbox with esmtpsa [Authenticated ID (1174703)] (TLS1.2:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.93) id 1taDIu-00BLdV-G3; Tue, 21 Jan 2025 13:24:24 +0100 From: Alexis Simon To: guix-patches@gnu.org Subject: [PATCH] gnu: Add r-sigfit. Date: Tue, 21 Jan 2025 13:23:32 +0100 Message-ID: X-Mailer: git-send-email 2.45.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a0c:5a00:149::26; envelope-from=alexis.simon@runbox.com; helo=mailtransmit05.runbox.com X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Alexis Simon 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 (r-sigfit): New variable. Change-Id: I9d63975d3512cf8583e7ec22f450bb4963c9ff2f --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c98f6022bf..899606b195 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1526,6 +1526,42 @@ (define-public r-saige tests in large cohorts and biobanks (SAIGE-GENE+).") (license license:gpl2+)))) +(define-public r-sigfit + (package + (name "r-sigfit") + (version "2.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kgori/sigfit") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16r6m8p90rnb4hxl86fz3kbals3626232i8fj0zhhd23p89z3w4v")))) + (properties `((upstream-name . "sigfit"))) + (build-system r-build-system) + (native-inputs (list r-codetools)) + (propagated-inputs (list r-rcpp + r-rstan + r-rstantools + r-coda + r-clue + r-knitr + r-rmarkdown + r-bh + r-rcppeigen + r-stanheaders)) + (home-page "https://github.com/kgori/sigfit") + (synopsis "Flexible Bayesian inference of mutational signatures") + (description + "R package to estimate signatures of mutational processes and their +activities on mutation count data. Starting from a set of single-nucleotide +variants (SNVs), it allows both estimation of the exposure of samples to +predefined mutational signatures (including whether the signatures are +present at all), and identification of signatures de novo from the mutation counts.") + (license license:gpl3))) + (define-public r-singlet (let ((commit "765a6c45081807a1522f0e8983e2417822a36f36") (revision "1")) base-commit: cf34ba66cf614358dfac925212d6a9074e318d80 -- 2.45.2 From debbugs-submit-bounces@debbugs.gnu.org Wed Jan 22 16:16:03 2025 Received: (at 75727-done) by debbugs.gnu.org; 22 Jan 2025 21:16:03 +0000 Received: from localhost ([127.0.0.1]:36850 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tai4x-0001NG-4R for submit@debbugs.gnu.org; Wed, 22 Jan 2025 16:16:03 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21167) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tai4t-0001Md-N5 for 75727-done@debbugs.gnu.org; Wed, 22 Jan 2025 16:16:00 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1737580556; cv=none; d=zohomail.com; s=zohoarc; b=FC24CVgk8QlEWnQYJwk+y0ChFqPNXeCFruQs/J/CkalJmCkOvK2cc1/b5xlHj0LoWbmBAjEjUUkOnp3kSCvdhjxpaSHbo8lpYf6iqvr0qqWxBqH4VJvKU2BHz1jLcjwQ34eDkbVaojfTLZbDU/JJSseyVZe2X0COpK2fQzVhTuo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1737580556; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=jscQxVKY94DNB4JEtnYOAP8EGk9qVOdQBxq/c1/H07Q=; b=CJA4WWA2I/OeZPupFU5MaKlQ75Yqy2Q4Qto4th8Ovne6VzbyCsXR09d7KDP5vaOanO9PiTvz4IRTh5suTZXqdJt11k9ZfFegSlWJ96PE4ckQH/NbWKtW/P8/2dP/NfotvcRSRneZZK83PydoPTVDv1X92kDZzIQ7Io6k38MfClI= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1737580556; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=jscQxVKY94DNB4JEtnYOAP8EGk9qVOdQBxq/c1/H07Q=; b=dBzdpSCQvGbhEuCvyvPZ//5yItFZ77v8TbbIK6DZRRGQldU7XkdD3We9ni1o61xl ewmTnJpgvhhkccJ5dV95fmE9C6uJK7om5/IuHgP/YDqvfiXlW/YG0fAobpi6hFhuYan BmWssOUljECniF6Q9oTuShFa8iSGw0uQ0UVSXV84= Received: by mx.zohomail.com with SMTPS id 173758055347316.38911033098873; Wed, 22 Jan 2025 13:15:53 -0800 (PST) From: Ricardo Wurmus To: 75727-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-sigfit. User-Agent: mu4e 1.12.7; emacs 29.4 Date: Wed, 22 Jan 2025 22:15:47 +0100 Message-ID: <87zfjia6t8.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 75727-done 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 (-) Thanks for the patch. Applied with commit cc678d0e4d67073943e75053c5e450c4df700b42 to the master branch. -- Ricardo From unknown Mon Aug 18 14:16:23 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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