From unknown Sat Jun 21 03:00:04 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#65688 <65688@debbugs.gnu.org> To: bug#65688 <65688@debbugs.gnu.org> Subject: Status: [PATCH 2/2] gnu: Add r-trackviewer. Reply-To: bug#65688 <65688@debbugs.gnu.org> Date: Sat, 21 Jun 2025 10:00:04 +0000 retitle 65688 [PATCH 2/2] gnu: Add r-trackviewer. reassign 65688 guix-patches submitter 65688 Navid Afkhami severity 65688 normal tag 65688 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Sep 01 16:45:45 2023 Received: (at submit) by debbugs.gnu.org; 1 Sep 2023 20:45:45 +0000 Received: from localhost ([127.0.0.1]:34166 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qcB1V-0004dJ-45 for submit@debbugs.gnu.org; Fri, 01 Sep 2023 16:45:45 -0400 Received: from lists.gnu.org ([2001:470:142::17]:34064) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qcB1S-0004Jf-5F for submit@debbugs.gnu.org; Fri, 01 Sep 2023 16:45:43 -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 1qcB1C-0005BY-T4 for guix-patches@gnu.org; Fri, 01 Sep 2023 16:45:27 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qcB19-00043z-FJ for guix-patches@gnu.org; Fri, 01 Sep 2023 16:45:26 -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=1693601121; x=1695415522; bh=m5BfyzifE6Ar4/jSzKlIvoUtIGhNPF0NNiYyWDwEHng=; b=NzxgfNv925wu bifxd1drAzVvlTpmohyJTyT4L7gCBpzCPzzoVfnm+G9l5/JXsKp2KsRpK+y0h54/ As4Rs35YRHE1wxicuMNByuv5YlyNhn+cV1134pwpp1GTlTFYvSwgbM4BIKStgahc qgUO1w5kpqUzdgrVLxxp9o829X2KzUk= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 2860FA026C for ; Fri, 1 Sep 2023 22:45:20 +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; Fri, 1 Sep 2023 22:45:20 +0200 From: Navid Afkhami To: Subject: [PATCH 2/2] gnu: Add r-trackviewer. Date: Fri, 1 Sep 2023 20:45:12 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: <646a45304d13b4544a475fc2ce490faee83496d8.1693601111.git.navid.afkhami@mdc-berlin.de> References: <646a45304d13b4544a475fc2ce490faee83496d8.1693601111.git.navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27850.002 X-TM-AS-Result: No-10--2.495400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEBJY j5KQbQRCuRqCCBRz7v/SiSwkWHlAYSq+GZ9ZHxIhuW77/y896siFzNNPDc6umOCbuVI7hVbLqbs +nJ/tFJGnxlJvDrfL8SeTbZ92Gn2xwCLgGsYLjVtHw6LwC7Gfetfta0VximgkU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DG1/c2gaIJKJc37Osy84zX1wx/3X5Whnz838A rdVgxLOF3OW1H4ixEU59MT3rL2YyizFIBOOluiX8mfqZUoQfVsxmFheDnahi2uLCTjzz6qi2qQa z8sERlrwQVgIdVG4FE5aD4ZIh+0xjhMO3DAp+0s= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.495400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27850.002 X-TM-SNTS-SMTP: ABE5F8E832FB268C960A56F7929B0F9A2042A1BCC65E01B2A7F71977C0A46A492000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.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-trackviewer): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 88592c4f71..0070d7777c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9931,6 +9931,48 @@ (define-public r-tkwidgets "This package implements widgets to provide user interfaces.") (license license:artistic2.0))) +(define-public r-trackviewer + (package + (name "r-trackviewer") + (version "1.36.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "trackViewer" version)) + (sha256 + (base32 + "1ngfpd308y8i3vgv07cggk2azs64lsyyc9zfi3pz0gapr33ha6a1")))) + (properties `((upstream-name . "trackViewer"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-biocgenerics + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-graph + r-grimport + r-gviz + r-htmlwidgets + r-interactionset + r-iranges + r-plotrix + r-rgraphviz + r-rhdf5 + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-strawr)) + (native-inputs (list esbuild r-knitr)) + (home-page "https://bioconductor.org/packages/trackViewer") + (synopsis "Web interface for interactive multi-omics data analysis") + (description + "TrackViewer offers multi-omics analysis with web based tracks and lollipops. +Visualize mapped reads along with annotation as track layers for NGS dataset +such as @code{ChIP-seq,} RNA-seq, @code{miRNA-seq,} DNA-seq, SNPs and +methylation data.") + (license license:gpl2+))) + (define-public r-transcriptr (package (name "r-transcriptr") -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Sep 02 05:57:44 2023 Received: (at 65688-done) by debbugs.gnu.org; 2 Sep 2023 09:57:44 +0000 Received: from localhost ([127.0.0.1]:35259 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qcNNv-0007cj-Va for submit@debbugs.gnu.org; Sat, 02 Sep 2023 05:57:44 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21187) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qcNNq-0007cX-LZ for 65688-done@debbugs.gnu.org; Sat, 02 Sep 2023 05:57:42 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1693648646; cv=none; d=zohomail.com; s=zohoarc; b=P/+ffXRh8ckrW2V6TWecI//a2Kw8eD5QmSHASW1L9Bfy3Azv5ujcPDG8emx/y/ZCDKZQPrPoBbbL4hW9wpzt2mUEebaNxGm4fPqSghhBkIm85LO5HNP4QuD3mhFOXTpsQ7hDVRJ8HyUx4013Kx3EsUa1zvjgyVw6qdJoIikYeVU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1693648646; h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To; bh=pvwReBwRmyusOPQturolXugG+Vf7MiRhYGmcnIOEGhQ=; b=H6pTnGGUzcR/tcLPEPiPw//jwx5SypOX19FPgv6TbF+LtTQMECzbux1CCrjpUaeMM0ok7ASz2gDqybgFEEIi3p1I3jSnyjF6MWoejnPQ8D9FJnCUISBMS2LFbFfu0g7iH1WydlC4tEHqUkWD/SmqJTAGcstYFKDchFoDHnmry3c= 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=1693648646; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=pvwReBwRmyusOPQturolXugG+Vf7MiRhYGmcnIOEGhQ=; b=SoFwQfUxjVP9zalhQWzJ4Zv38Q3YceKvhYlWj5g4kSOaI2GBzwHE30NE7TSgA4nv uyMZvkppUx+J2WMdEyaA1mTUGzCbRxw9L7+/R5T98uywPGn6WwQyOqOA3IeZD/DQ0bm HZMgCBkBnQJM8i9AiK9+3Xd5HQlKRt9vVgI05gso= Received: from localhost (113-111-142-46.pool.kielnet.net [46.142.111.113]) by mx.zohomail.com with SMTPS id 1693648643676592.0179586798458; Sat, 2 Sep 2023 02:57:23 -0700 (PDT) User-agent: mu4e 1.10.5; emacs 28.2 From: Ricardo Wurmus To: 65688-done@debbugs.gnu.org Subject: [PATCH 2/2] gnu: Add r-trackviewer. Date: Sat, 02 Sep 2023 11:55:55 +0200 Message-ID: <87h6ocdhj3.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 65688-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! This one needed a little more work. The =E2=80=9Cesbuild=E2=80=9D in the n= ative inputs was added by the importer because the package includes minified JavaScript files. Luckily it=E2=80=99s just one file and we can replace it easily. I=E2=80= =99ve made the necessary changes and pushed it with commit 8c0c94bf9f70a9252cd6f4261d2bce6bdba2bd0b to the =E2=80=9Cmaster=E2=80=9D br= anch. --=20 Ricardo From unknown Sat Jun 21 03:00:04 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 30 Sep 2023 11:24:33 +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