From unknown Mon Jun 23 00:37:15 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#56141] [PATCH] gnu: Add r-asafe. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 22 Jun 2022 13:47:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 56141 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 56141@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16559055754548 (code B ref -1); Wed, 22 Jun 2022 13:47:02 +0000 Received: (at submit) by debbugs.gnu.org; 22 Jun 2022 13:46:15 +0000 Received: from localhost ([127.0.0.1]:34439 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o40gR-0001BI-34 for submit@debbugs.gnu.org; Wed, 22 Jun 2022 09:46:15 -0400 Received: from lists.gnu.org ([209.51.188.17]:47484) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o40gO-0001B9-US for submit@debbugs.gnu.org; Wed, 22 Jun 2022 09:46:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48610) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o40gO-00037j-C6 for guix-patches@gnu.org; Wed, 22 Jun 2022 09:46:12 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:51659) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o40gL-000799-P8 for guix-patches@gnu.org; Wed, 22 Jun 2022 09:46:11 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 1D828160362 for ; Wed, 22 Jun 2022 15:45:50 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1655905549; x=1657719950; bh=1/v5DZHmhpBeBFm8rhSX5d3gGwTwQRJxS66xPDNLvtQ=; b=lnHqCEc3K2ct NvReDstTomYSqpb9ZDNMgsVSBVZtkel1S9pr9Jfb0kzuSXTUgdQh0kAiwuDlpNwY FMg9Jb4IY1MVAkeVBVSWnljI4b9sZ+jU08xQ60VtaScsLDZ2aQdvrJxu2NZRfrJZ +h+ZLy6zZuO0QzUSmWopiq25fXUbh0Y= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id pqnGzeYkXHwT for ; Wed, 22 Jun 2022 15:45:49 +0200 (CEST) Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Wed, 22 Jun 2022 15:45:49 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Wed, 22 Jun 2022 15:45:48 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Wed, 22 Jun 2022 15:45:33 +0200 Message-ID: <20220622134533.15458-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-AS-Result: No-10--3.531200-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCzLRD51bz5RZOuLH9BII+4qrKs axUiN/ykX0jceDJtHIX6VxxWFgkHXo8WMkQWv6iUGJ4JQFnQmG42j49Ftap9Eymsk/wUE4hrdPm 6Zo4+L6uHRskZfSnnYydTVVWwhxWOAOV329uWnA0JZwpEaPI/JtgLV27rR2yEFbtiGtaho67NvB ssOMTECNUmgJg++gCbjbMXojSkk1rTnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.531200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-SNTS-SMTP: C378852F4AC19A6D58F6B03F7C8350E328A2AF4C015A9FC00AEEF096F1D019202002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-asafe): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..2d199a79f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,28 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-asafe + (package + (name "r-asafe") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASAFE" version)) + (sha256 + (base32 + "1l9iqw2imr6w2gwqrmg05jp6lj2xc7hbyhd144d4q8vw8z7ga4ns")))) + (properties `((upstream-name . "ASAFE"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASAFE") + (synopsis "Ancestry Specific Allele Frequency Estimation") + (description + "The @code{ASAFE} package contains a collection of functions that can be used +to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate ancestry +-specific allele frequencies for a bi-allelic genetic marker, e.g. an @dfn{SNP} +(single nucleotide polymorphism) from genotypes and ancestry pairs.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 -- 2.36.1 From unknown Mon Jun 23 00:37:15 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: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Subject: bug#56141: closed ([PATCH] gnu: Add r-asafe.) Message-ID: References: <87leo0o3fr.fsf@elephly.net> <20220622134533.15458-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 56141 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 56141@debbugs.gnu.org Date: Thu, 24 Nov 2022 14:04:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1669298642-22118-1" This is a multi-part message in MIME format... ------------=_1669298642-22118-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #56141: [PATCH] gnu: Add r-asafe. 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 56141@debbugs.gnu.org. --=20 56141: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D56141 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1669298642-22118-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 56141-done) by debbugs.gnu.org; 24 Nov 2022 14:03:11 +0000 Received: from localhost ([127.0.0.1]:57763 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyCoo-0005jh-T5 for submit@debbugs.gnu.org; Thu, 24 Nov 2022 09:03:11 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21178) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyCom-0005jW-SL for 56141-done@debbugs.gnu.org; Thu, 24 Nov 2022 09:03:09 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1669298587; cv=none; d=zohomail.com; s=zohoarc; b=GDliOuZElNbdOWgtMU8f7RfvVKrq6iuzpkP/eOjmqLxu9JITuSArnpiKwdFSTWA106dKLw0X6w+Cg72jYGbYooAguw2wFiglqjqO16zmM83H6L/DJ7SA56H8slk3Q4YEWEH5SCG9axz/DZLYBiz1qMGfvMjpH+RwA15PWpguLGo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1669298587; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=HLgQD2XdHn/ivyi0bZfoldAPnVtI8WVwWxLsfFH6sXCjdBvDXAfU5SVniaJNk+x4m7QffSn/fODmmWC5Gba2Mm0sFlYWGGIOEGzegwlLW7YpTFsiAkiGEbAzocHIqxAZQhWz48aYrtcxOw/OCO6NeF1JOtIG5jhxhQWiW57Py+g= 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=1669298587; 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=VG1LAp/EGbsdBwo79AT5alOgM25zAG9b1t+IIDa4dWU=; b=Q7spNd0fCjbp+HuSVFSuoBHyfVXei1ECQNs/cC3fhxzp9gfIWt200zk6wYDSSqf9 qwEisYZ/z2KlHLrrgywVElvV9XZ9/jlcGfOy70sNHvKluDkjFq3mimk9rphOPJYtrvx JMrSKeUB5mKiQtee5cQt8hngLWQgKI3g1JexqUy8= Received: from localhost (145-109-142-46.pool.kielnet.net [46.142.109.145]) by mx.zohomail.com with SMTPS id 1669298586649638.0559278803901; Thu, 24 Nov 2022 06:03:06 -0800 (PST) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 56141-done@debbugs.gnu.org Subject: [PATCH] gnu: Add r-asafe. Date: Thu, 24 Nov 2022 15:02:51 +0100 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 Message-ID: <87leo0o3fr.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 56141-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 (-) Applied, thanks! -- Ricardo ------------=_1669298642-22118-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 22 Jun 2022 13:46:15 +0000 Received: from localhost ([127.0.0.1]:34439 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o40gR-0001BI-34 for submit@debbugs.gnu.org; Wed, 22 Jun 2022 09:46:15 -0400 Received: from lists.gnu.org ([209.51.188.17]:47484) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o40gO-0001B9-US for submit@debbugs.gnu.org; Wed, 22 Jun 2022 09:46:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48610) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o40gO-00037j-C6 for guix-patches@gnu.org; Wed, 22 Jun 2022 09:46:12 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:51659) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o40gL-000799-P8 for guix-patches@gnu.org; Wed, 22 Jun 2022 09:46:11 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 1D828160362 for ; Wed, 22 Jun 2022 15:45:50 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1655905549; x=1657719950; bh=1/v5DZHmhpBeBFm8rhSX5d3gGwTwQRJxS66xPDNLvtQ=; b=lnHqCEc3K2ct NvReDstTomYSqpb9ZDNMgsVSBVZtkel1S9pr9Jfb0kzuSXTUgdQh0kAiwuDlpNwY FMg9Jb4IY1MVAkeVBVSWnljI4b9sZ+jU08xQ60VtaScsLDZ2aQdvrJxu2NZRfrJZ +h+ZLy6zZuO0QzUSmWopiq25fXUbh0Y= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id pqnGzeYkXHwT for ; Wed, 22 Jun 2022 15:45:49 +0200 (CEST) Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Wed, 22 Jun 2022 15:45:49 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Wed, 22 Jun 2022 15:45:48 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-asafe. Date: Wed, 22 Jun 2022 15:45:33 +0200 Message-ID: <20220622134533.15458-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-AS-Result: No-10--3.531200-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCzLRD51bz5RZOuLH9BII+4qrKs axUiN/ykX0jceDJtHIX6VxxWFgkHXo8WMkQWv6iUGJ4JQFnQmG42j49Ftap9Eymsk/wUE4hrdPm 6Zo4+L6uHRskZfSnnYydTVVWwhxWOAOV329uWnA0JZwpEaPI/JtgLV27rR2yEFbtiGtaho67NvB ssOMTECNUmgJg++gCbjbMXojSkk1rTnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.531200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26970.005 X-TM-SNTS-SMTP: C378852F4AC19A6D58F6B03F7C8350E328A2AF4C015A9FC00AEEF096F1D019202002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-asafe): New variable. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..2d199a79f2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,28 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-asafe + (package + (name "r-asafe") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ASAFE" version)) + (sha256 + (base32 + "1l9iqw2imr6w2gwqrmg05jp6lj2xc7hbyhd144d4q8vw8z7ga4ns")))) + (properties `((upstream-name . "ASAFE"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ASAFE") + (synopsis "Ancestry Specific Allele Frequency Estimation") + (description + "The @code{ASAFE} package contains a collection of functions that can be used +to carry out an @dfn{EM} (Expectation–maximization) algorithm to estimate ancestry +-specific allele frequencies for a bi-allelic genetic marker, e.g. an @dfn{SNP} +(single nucleotide polymorphism) from genotypes and ancestry pairs.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: e74fa406e1043547242a8b67ab9907fea7aae6b9 -- 2.36.1 ------------=_1669298642-22118-1--