From unknown Sun Jun 22 11:39:40 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 24 Aug 2023 13:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 65500 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 65500@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169288374522283 (code B ref -1); Thu, 24 Aug 2023 13:30:02 +0000 Received: (at submit) by debbugs.gnu.org; 24 Aug 2023 13:29:05 +0000 Received: from localhost ([127.0.0.1]:36385 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOW-0005nL-Mn for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:29:05 -0400 Received: from lists.gnu.org ([2001:470:142::17]:55966) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOU-0005mm-Hq for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:29:03 -0400 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 1qZAOI-0004ss-BP for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:51 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qZAOF-0004Hf-Oc for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:50 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1692883724; x=1694698125; bh=cLOAy6V9r7ftjSfWBlwGYV1T6bdUteTp5LMhsPgw1Ug=; b=l42BNeKz74E/ QVI68gSSRlJr/dBqm1KTJN3doDUbF1Z2ht3EHR1c9+TrZV2YcMuwvHTGrqQ56LUt E4osRMKWHpC6PWtjXCQYp21CIq3S5f2YkkDFKFlRtMgoAtcssEgktuQme9N9K+z3 73BPAxAPbpd9YSQWLMP8hZldQBlDzPo= 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 id CC5F616034E for ; Thu, 24 Aug 2023 15:28:44 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.32; Thu, 24 Aug 2023 15:28:44 +0200 From: Navid Afkhami Date: Thu, 24 Aug 2023 13:28:28 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-AS-Result: No-10--3.113400-5.000000 X-TMASE-MatchedRID: JUGAxiLh1cP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZL9Yv7P2J5iwmA0 yITMNzjl9LQinZ4QefPcjNeVeWlqY+gtHj7OwNO22utO5qEfOUdARBOrTIjN2Y4wgQ05hcUMzww 9tSb2RaGR2/d8xMND2Xzt7UAp5umA2DUaxs6FR5E7JKKPALJUtfBs3rZsh/GcXAvh586il4W/H7 LhIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgPpCuffGH9zI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.113400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-SNTS-SMTP: F18E0FDAC4FAF4C20F649067E2E4CF8EFC7A36BCDD5A6048498EACB72457B7ED2000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) 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/bioconductor.scm (r-mousegastrulationdata): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6204173277..f3671e5cca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8009,6 +8009,37 @@ (define-public r-motifrg throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mousegastrulationdata + (package + (name "r-mousegastrulationdata") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "MouseGastrulationData" version + 'experiment)) + (sha256 + (base32 + "155kci5isq7mlbvv8mdl2jjpafm3pbv1likhls70aa746spr1h17")))) + (properties `((upstream-name . "MouseGastrulationData"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-bumpymatrix + r-experimenthub + r-s4vectors + r-singlecellexperiment + r-spatialexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/MarioniLab/MouseGastrulationData") + (synopsis + "Single-Cell omics data across mouse gastrulation and early organogenesis") + (description + "This package provides processed and raw count data for single-cell RNA sequencing. +in addition, this package offers single-cell ATAC-seq, and @code{seqFISH} +(spatial transcriptomic) experiments performed along a timecourse of mouse +gastrulation and early organogenesis.") + (license license:gpl3))) + (define-public r-muscat (package (name "r-muscat") -- 2.34.1 From unknown Sun Jun 22 11:39:40 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: Navid Afkhami Subject: bug#65500: closed ([PATCH 2/2] gnu: Add r-mousegastrulationdata.) Message-ID: References: <878r9vfugd.fsf@elephly.net> X-Gnu-PR-Message: they-closed 65500 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 65500@debbugs.gnu.org Date: Mon, 28 Aug 2023 08:22:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1693210923-10292-1" This is a multi-part message in MIME format... ------------=_1693210923-10292-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #65500: [PATCH 2/2] gnu: Add r-mousegastrulationdata. 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 65500@debbugs.gnu.org. --=20 65500: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D65500 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1693210923-10292-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 65500-done) by debbugs.gnu.org; 28 Aug 2023 08:21:52 +0000 Received: from localhost ([127.0.0.1]:46877 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qaXVQ-0002fO-6o for submit@debbugs.gnu.org; Mon, 28 Aug 2023 04:21:52 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21020) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qaXVO-0002fG-M9 for 65500-done@debbugs.gnu.org; Mon, 28 Aug 2023 04:21:51 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1693210901; cv=none; d=zohomail.com; s=zohoarc; b=ELPeASpkMT+2TdP4XVpqkG4z88H1Wpz0Qy5902Lzf4KT4fVr6T94EJzEW0pqPq1t3w2d8n2+YdB/VSD4VHwoAcWS0FY+8R43Uvla2Z5Ge4taBcicgcOfZBaLGBOkkuwpnCNIHoMrZx6jf/g7fnOKNn/8R/sIvge/gpXHNzOHDws= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1693210901; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=E/qxD3d05lq7svrKI6MBtzs3jam2f7Jst0UluIgH/9s=; b=CtfcYIZTAN6RHlZquqgXxi/i8hhF5Nh0vP/+2SCgDHBswvWi8AdbwCjSZk3vEOw0CGQ9vufz2v2rb1NjmE6m685R/gStLQpKrpMZFUy5zb+CygrTHu27d4SRVJ00gNskP3xxWO9IIU4iV1jSfC3PxGtRCnEb+gfKP9z0/Kw+zgg= 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=1693210901; 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=E/qxD3d05lq7svrKI6MBtzs3jam2f7Jst0UluIgH/9s=; b=TD2tMQsaNCI0IgsEOsnTBGe3RZc1BZge09d78qUME4kBW58IgIocbQVkHyS8eGqa D1YWd66b+jsRxNyKvN2Q64yXO/cAdV8zOuXOkLIlxLMLVuVmh5OCS2UwMyJj7bUPJP3 MVnlcCnDODJwuUPFQXTIgSJX+HRcj9MMSrG829Dc= Received: from localhost (113-111-142-46.pool.kielnet.net [46.142.111.113]) by mx.zohomail.com with SMTPS id 1693210900837356.3515911142879; Mon, 28 Aug 2023 01:21:40 -0700 (PDT) User-agent: mu4e 1.10.5; emacs 28.2 From: Ricardo Wurmus To: 65500-done@debbugs.gnu.org Subject: [PATCH 2/2] gnu: Add r-mousegastrulationdata. Date: Mon, 28 Aug 2023 10:20:56 +0200 Message-ID: <878r9vfugd.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 65500-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 with minor changes: - location in the file, next to other experiment packages - formatting of the description. -- Ricardo ------------=_1693210923-10292-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 24 Aug 2023 13:29:05 +0000 Received: from localhost ([127.0.0.1]:36385 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOW-0005nL-Mn for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:29:05 -0400 Received: from lists.gnu.org ([2001:470:142::17]:55966) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qZAOU-0005mm-Hq for submit@debbugs.gnu.org; Thu, 24 Aug 2023 09:29:03 -0400 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 1qZAOI-0004ss-BP for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:51 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qZAOF-0004Hf-Oc for guix-patches@gnu.org; Thu, 24 Aug 2023 09:28:50 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1692883724; x=1694698125; bh=cLOAy6V9r7ftjSfWBlwGYV1T6bdUteTp5LMhsPgw1Ug=; b=l42BNeKz74E/ QVI68gSSRlJr/dBqm1KTJN3doDUbF1Z2ht3EHR1c9+TrZV2YcMuwvHTGrqQ56LUt E4osRMKWHpC6PWtjXCQYp21CIq3S5f2YkkDFKFlRtMgoAtcssEgktuQme9N9K+z3 73BPAxAPbpd9YSQWLMP8hZldQBlDzPo= 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 id CC5F616034E for ; Thu, 24 Aug 2023 15:28:44 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.32; Thu, 24 Aug 2023 15:28:44 +0200 From: Navid Afkhami To: Subject: [PATCH 2/2] gnu: Add r-mousegastrulationdata. Date: Thu, 24 Aug 2023 13:28:28 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-AS-Result: No-10--3.113400-5.000000 X-TMASE-MatchedRID: JUGAxiLh1cP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZL9Yv7P2J5iwmA0 yITMNzjl9LQinZ4QefPcjNeVeWlqY+gtHj7OwNO22utO5qEfOUdARBOrTIjN2Y4wgQ05hcUMzww 9tSb2RaGR2/d8xMND2Xzt7UAp5umA2DUaxs6FR5E7JKKPALJUtfBs3rZsh/GcXAvh586il4W/H7 LhIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgPpCuffGH9zI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.113400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27832.007 X-TM-SNTS-SMTP: F18E0FDAC4FAF4C20F649067E2E4CF8EFC7A36BCDD5A6048498EACB72457B7ED2000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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/bioconductor.scm (r-mousegastrulationdata): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6204173277..f3671e5cca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8009,6 +8009,37 @@ (define-public r-motifrg throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mousegastrulationdata + (package + (name "r-mousegastrulationdata") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "MouseGastrulationData" version + 'experiment)) + (sha256 + (base32 + "155kci5isq7mlbvv8mdl2jjpafm3pbv1likhls70aa746spr1h17")))) + (properties `((upstream-name . "MouseGastrulationData"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-bumpymatrix + r-experimenthub + r-s4vectors + r-singlecellexperiment + r-spatialexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/MarioniLab/MouseGastrulationData") + (synopsis + "Single-Cell omics data across mouse gastrulation and early organogenesis") + (description + "This package provides processed and raw count data for single-cell RNA sequencing. +in addition, this package offers single-cell ATAC-seq, and @code{seqFISH} +(spatial transcriptomic) experiments performed along a timecourse of mouse +gastrulation and early organogenesis.") + (license license:gpl3))) + (define-public r-muscat (package (name "r-muscat") -- 2.34.1 ------------=_1693210923-10292-1--