From unknown Wed Jun 25 00:27:14 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#57338] [PATCH] gnu: Add r-parathyroidse. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Mon, 22 Aug 2022 10:34:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 57338 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 57338@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.166116443312036 (code B ref -1); Mon, 22 Aug 2022 10:34:02 +0000 Received: (at submit) by debbugs.gnu.org; 22 Aug 2022 10:33:53 +0000 Received: from localhost ([127.0.0.1]:38013 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ4kj-000384-9p for submit@debbugs.gnu.org; Mon, 22 Aug 2022 06:33:53 -0400 Received: from lists.gnu.org ([209.51.188.17]:54340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ4kh-00037w-9w for submit@debbugs.gnu.org; Mon, 22 Aug 2022 06:33:52 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:44428) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ4kV-0006L0-J8 for guix-patches@gnu.org; Mon, 22 Aug 2022 06:33:48 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:49257) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ4kQ-0005FR-F9 for guix-patches@gnu.org; Mon, 22 Aug 2022 06:33:37 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1661164410; x=1662978811; bh=eFhqKpFCyVHXOt5 w7DEKOGDcZ+uZmRrdnDm2c8tJyCw=; b=EMV4zMAbOSzzgCPmqz5cKzaxjU2ygzN 0KCnDjswFdnyq7KeHu+ugyLuiWNM74Wy9Oi23bAIfZOn70sArDR0myN3mxqYoksl Ud/6yRZb8rt8KaHcd7Dy30qBTxPsieIV4G08snUl9kVyChEAxoOeG7UWttSGFYyu ZbCljaO17bRs= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id E4B8116034A for ; Mon, 22 Aug 2022 12:33:29 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.12; Mon, 22 Aug 2022 12:33:29 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 22 Aug 2022 12:33:19 +0200 Message-ID: <20220822103319.29907-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-AS-Result: No-10--7.752300-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZHd17Y6gGqDCycO hvTXTlouSkIUZyUQUJxJTjjs9yT6Yo8WMkQWv6iUoTQl7wNH8Po2j49Ftap9Eymsk/wUE4hoZ/c xLmjjItxnNzYjZAjykEXjBEdecGhOkgHGPRDib2c301fLtnixf X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.752300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-SNTS-SMTP: 0EE6B762074D490F649C615DEAF7843B567925021EFA08571E311149DD32A26C2002: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-parathyroidse): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d2ca413e9..b4f880a080 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1541,6 +1541,30 @@ (define-public r-curatedtcgadata across the entire multi-'omics experiment.") (license license:artistic2.0))) +(define-public r-parathyroidse + (package + (name "r-parathyroidse") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "parathyroidSE" version + 'experiment)) + (sha256 + (base32 + "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16")))) + (properties `((upstream-name . "parathyroidSE"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (home-page "https://bioconductor.org/packages/parathyroidSE") + (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors") + (description + "This package provides @code{RangedSummarizedExperiment} objects of read +counts in genes and exonic parts for paired-end RNA-Seq data from experiments on +primary cultures of parathyroid tumors. The sequencing was performed on tumor +cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).") + ;; The author(s) mentions only LGPL without any specific version. + (license license:lgpl2.1+))) + (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") base-commit: 706b3ef38b2f7ce9f05aa56e2eaaaf1c19e25f90 -- 2.37.2 From unknown Wed Jun 25 00:27:14 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#57338: closed (Re: [bug#57338] [PATCH] gnu: Add r-parathyroidse.) Message-ID: References: <87sflnz3nm.fsf@elephly.net> <20220822103319.29907-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 57338 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 57338@debbugs.gnu.org Date: Tue, 23 Aug 2022 09:55:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1661248502-20393-1" This is a multi-part message in MIME format... ------------=_1661248502-20393-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #57338: [PATCH] gnu: Add r-parathyroidse. 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 57338@debbugs.gnu.org. --=20 57338: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D57338 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1661248502-20393-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 57338-done) by debbugs.gnu.org; 23 Aug 2022 09:54:22 +0000 Received: from localhost ([127.0.0.1]:42636 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQQc1-0005Hq-Lu for submit@debbugs.gnu.org; Tue, 23 Aug 2022 05:54:22 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21032) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQQbr-0005HY-Rx for 57338-done@debbugs.gnu.org; Tue, 23 Aug 2022 05:54:13 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1661248450; cv=none; d=zohomail.com; s=zohoarc; b=FrYInnBXd18k5J6rNcd3AVdB7wFjbID16gX+fl3qV/YkabT6nA7kIRP59DcJVhNsLGHPK37lKMI1GNeGBwM0XfewUvdmor5MHhSt9DkYYdwTN/77ENRzJFO/9al9xu+ofTyXPgQRdfEXT7L4yc3/JJDZHIO6+UGq7dk2pawoLxc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1661248450; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=WLdDO1bl9asjaVRUKzlFnjE4h9l8i9ioB985J8SLxv8=; b=j0lzgAsR/nxB2hTRxwUbdMBsZoKLpDTbZvZVHLfQD/RxxPktgAzIHYUdCBZSCwUH7iQyVlts5O3VkDQTZk18WAsq5ynFGs5ystRKmh2TkpQzJzrTBjOsrDQU6ABK0BV4IfmjDQmsnQ7bwLzaywIp8GD1ATlHJywIwnnImqbdqXU= 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=1661248450; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=WLdDO1bl9asjaVRUKzlFnjE4h9l8i9ioB985J8SLxv8=; b=WTUfW60dlR1AgFdg01i4oaG+TSp4apOzsV9YKnqBxprPuc3jr4Dl6yZiRSzpaw4L L3Dm3EvfoPymVpAW78D+nmciqvD1DDeCaNqzkgVQRani/MwTWOBGtpmLevv5TfNDbkx Vb3hHeZfZtYXTeEyE4kXEOoW8czEXyCC18N4FOUU= Received: from localhost (84-109-142-46.pool.kielnet.net [46.142.109.84]) by mx.zohomail.com with SMTPS id 1661248447954465.03894661983827; Tue, 23 Aug 2022 02:54:07 -0700 (PDT) References: <20220822103319.29907-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.7; emacs 28.1 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#57338] [PATCH] gnu: Add r-parathyroidse. Date: Tue, 23 Aug 2022 11:53:52 +0200 In-reply-to: <20220822103319.29907-1-madalinionel.patrascu@mdc-berlin.de> 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: <87sflnz3nm.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: 57338-done Cc: 57338-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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioconductor.scm (r-parathyroidse): New variable. Applied, thanks! --=20 Ricardo ------------=_1661248502-20393-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 22 Aug 2022 10:33:53 +0000 Received: from localhost ([127.0.0.1]:38013 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ4kj-000384-9p for submit@debbugs.gnu.org; Mon, 22 Aug 2022 06:33:53 -0400 Received: from lists.gnu.org ([209.51.188.17]:54340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oQ4kh-00037w-9w for submit@debbugs.gnu.org; Mon, 22 Aug 2022 06:33:52 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:44428) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ4kV-0006L0-J8 for guix-patches@gnu.org; Mon, 22 Aug 2022 06:33:48 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:49257) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oQ4kQ-0005FR-F9 for guix-patches@gnu.org; Mon, 22 Aug 2022 06:33:37 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1661164410; x=1662978811; bh=eFhqKpFCyVHXOt5 w7DEKOGDcZ+uZmRrdnDm2c8tJyCw=; b=EMV4zMAbOSzzgCPmqz5cKzaxjU2ygzN 0KCnDjswFdnyq7KeHu+ugyLuiWNM74Wy9Oi23bAIfZOn70sArDR0myN3mxqYoksl Ud/6yRZb8rt8KaHcd7Dy30qBTxPsieIV4G08snUl9kVyChEAxoOeG7UWttSGFYyu ZbCljaO17bRs= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id E4B8116034A for ; Mon, 22 Aug 2022 12:33:29 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.12; Mon, 22 Aug 2022 12:33:29 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-parathyroidse. Date: Mon, 22 Aug 2022 12:33:19 +0200 Message-ID: <20220822103319.29907-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.2 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-AS-Result: No-10--7.752300-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZHd17Y6gGqDCycO hvTXTlouSkIUZyUQUJxJTjjs9yT6Yo8WMkQWv6iUoTQl7wNH8Po2j49Ftap9Eymsk/wUE4hoZ/c xLmjjItxnNzYjZAjykEXjBEdecGhOkgHGPRDib2c301fLtnixf X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.752300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27092.007 X-TM-SNTS-SMTP: 0EE6B762074D490F649C615DEAF7843B567925021EFA08571E311149DD32A26C2002: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-parathyroidse): New variable. --- gnu/packages/bioconductor.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7d2ca413e9..b4f880a080 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1541,6 +1541,30 @@ (define-public r-curatedtcgadata across the entire multi-'omics experiment.") (license license:artistic2.0))) +(define-public r-parathyroidse + (package + (name "r-parathyroidse") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "parathyroidSE" version + 'experiment)) + (sha256 + (base32 + "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16")))) + (properties `((upstream-name . "parathyroidSE"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (home-page "https://bioconductor.org/packages/parathyroidSE") + (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors") + (description + "This package provides @code{RangedSummarizedExperiment} objects of read +counts in genes and exonic parts for paired-end RNA-Seq data from experiments on +primary cultures of parathyroid tumors. The sequencing was performed on tumor +cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).") + ;; The author(s) mentions only LGPL without any specific version. + (license license:lgpl2.1+))) + (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") base-commit: 706b3ef38b2f7ce9f05aa56e2eaaaf1c19e25f90 -- 2.37.2 ------------=_1661248502-20393-1--