From unknown Sat Jun 21 05:19:31 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#54903] [PATCH] gnu: r-catalyst: Update to 1.18.1. 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, 13 Apr 2022 11:22:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 54903 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54903@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16498488912260 (code B ref -1); Wed, 13 Apr 2022 11:22:02 +0000 Received: (at submit) by debbugs.gnu.org; 13 Apr 2022 11:21:31 +0000 Received: from localhost ([127.0.0.1]:51850 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neb3z-0000aN-8c for submit@debbugs.gnu.org; Wed, 13 Apr 2022 07:21:31 -0400 Received: from lists.gnu.org ([209.51.188.17]:44606) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neb3x-0000aF-Tj for submit@debbugs.gnu.org; Wed, 13 Apr 2022 07:21:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42654) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neb3x-0000GN-N4 for guix-patches@gnu.org; Wed, 13 Apr 2022 07:21:29 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:51701) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neb3t-0000Oa-Gl for guix-patches@gnu.org; Wed, 13 Apr 2022 07:21:28 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 69A5F160167 for ; Wed, 13 Apr 2022 13:21:21 +0200 (CEST) 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:received:received; s=mdc; t=1649848880; x=1651663281; bh=Sf9vzwxCbO5Jj/rbqjs+b1qo/wGl0E+MdRJmWjf6k/0=; b=QlKmC+it9R00 wNq7KT0EjCtVdATACRHDi86t4srjUnXaNo0ykHC8iCrHzn+wUNMtD9vS+Ht3gMf1 bt3c77SzDs5v0+Dzf+aZqyGcIM2Aqpkqy6ABRd2A2clBp1fIBMarZGvXQ1VcdUip syN0KZRHLxUu3ktbtU1mi54cczzFrEk= 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 OjWsV8F7PC7u for ; Wed, 13 Apr 2022 13:21:20 +0200 (CEST) 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 for ; Wed, 13 Apr 2022 13:21:20 +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 15.1.2375.24; Wed, 13 Apr 2022 13:21:20 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Wed, 13 Apr 2022 13:21:03 +0200 Message-ID: <20220413112103.26787-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1000-26830.007 X-TM-AS-Result: No-10--5.266400-5.000000 X-TMASE-MatchedRID: YkRLh4oRGObshae+2j71naoXHZz/dXlxbDYaN6olIzbAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/B7pmY37wJXiIqpZjtBYB7Dc/ RMZVpK/a1kNWgxodwXpJkLwIJ/8mP1pVckLHgk0Krm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGjNpc4k18Mbt2MBSXbYk3aCg3xm812tzYfChzAAZWmmtdPboNB0PB7k= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.266400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1000-26830.007 X-TM-SNTS-SMTP: 865CF350D3983B720A461D0C7B61FB4DBCBCBBB7481DD19FE29975DB6A5BA9952000: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-catalyst): Update to 1.18.1. [description]: Add Texinfo markups and clarify a sentence. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++------------ 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803437a033..d57a09f39d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13786,14 +13786,14 @@ (define-public r-msmstests (define-public r-catalyst (package (name "r-catalyst") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi")))) + "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -13829,16 +13829,23 @@ (define-public r-catalyst "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") (description - "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass -cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as -reporters to label antibodies, thereby substantially decreasing spectral -overlap and allowing for examination of over 50 parameters at the single cell -level. While spectral overlap is significantly less pronounced in CyTOF than -flow cytometry, spillover due to detection sensitivity, isotopic impurities, -and oxide formation can impede data interpretability. We designed -CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for -preprocessing of cytometry data, including i) normalization using bead -standards, ii) single-cell deconvolution, and iii) bead-based compensation.") + "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass +cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal +isotopes rather than fluorescent tags as reporters to label antibodies, thereby +substantially decreasing spectral overlap and allowing for examination of over +50 parameters at the single cell level. While spectral overlap is +significantly less pronounced in CyTOF than flow cytometry, spillover due to +detection sensitivity, isotopic impurities, and oxide formation can impede data +interpretability. We designed @code{CATALYST} to provide a pipeline for +preprocessing of cytometry data, including: +@enumerate +@item +normalization using bead standards; +@item +single-cell deconvolution; +@item +bead-based compensation. +@end enumerate") (license license:gpl2+))) (define-public r-erma -- 2.34.0 From unknown Sat Jun 21 05:19:31 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#54903: closed ([PATCH] gnu: r-catalyst: Update to 1.18.1.) Message-ID: References: <878rs8xaj3.fsf@elephly.net> <20220413112103.26787-1-madalinionel.patrascu@mdc-berlin.de> X-Gnu-PR-Message: they-closed 54903 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 54903@debbugs.gnu.org Date: Thu, 14 Apr 2022 09:47:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1649929622-12247-1" This is a multi-part message in MIME format... ------------=_1649929622-12247-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #54903: [PATCH] gnu: r-catalyst: Update to 1.18.1. 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 54903@debbugs.gnu.org. --=20 54903: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D54903 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1649929622-12247-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 54903-done) by debbugs.gnu.org; 14 Apr 2022 09:46:33 +0000 Received: from localhost ([127.0.0.1]:55197 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1new3d-0003An-23 for submit@debbugs.gnu.org; Thu, 14 Apr 2022 05:46:33 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21155) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1new3b-0003Ae-17 for 54903-done@debbugs.gnu.org; Thu, 14 Apr 2022 05:46:32 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649929588; cv=none; d=zohomail.com; s=zohoarc; b=jeFFbZQRkTAfLM7Bfgrdjxm2NhVmy8t/+8kYMF0bmQOVOz/x3o8iwfzjMWIa57ckroHCA1trCxmRj7b0U2st1fl8RMEPIIVZs2aTOcYq5oKbFOfDEUSNJu4J5AzSqFJ7GWH/hXqHWzbHP8z0lj27qiBrj49NeyLHYkXMjavHAKk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649929588; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=JyhQsMQYeNIbKHrBN2nCdJK5aSF2tnL8A7Szx0x1fjo=; b=Rzz9sftkOLNMkePSv2/70+wlmB82d/dhetUwzn6vFXwXF07xztIezUDVDftk/4tgJXkhWhmoBMG+oWs1gyK991XL5/VufVVDIrTsmzKrrvATYVrs9nrq6tJbGMUhpSQPqNGr8lcsuMBAo/QqitBtAJ/hEtziMRe15i22K8KHlJw= 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=1649929588; 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=JyhQsMQYeNIbKHrBN2nCdJK5aSF2tnL8A7Szx0x1fjo=; b=LtbruA63s+626Vuy7IckdkErPKPUVsYS3PAwcyPXmeWLsouHiuHuSbbER5JAW3qy klpuGf4ylV/y+FN+dqbb0rV8wP2UD+QLCqBjnkOUu7u3DTCC/lQZgj01w57ZRK+aTRk 4tz+lW9ps6hVfLoOoE/TpQrrw18xXFiawLW41C2w= Received: from localhost (152-108-142-46.pool.kielnet.net [46.142.108.152]) by mx.zohomail.com with SMTPS id 1649929587412189.2089012434011; Thu, 14 Apr 2022 02:46:27 -0700 (PDT) User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: 54903-done@debbugs.gnu.org Subject: [PATCH] gnu: r-catalyst: Update to 1.18.1. Date: Thu, 14 Apr 2022 11:44:58 +0200 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: <878rs8xaj3.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54903-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. I edited the description a little bit and applied it. Since I already made a bulk upgrade of all Bioconductor packages (better to keep them all in sync) I edited the commit message to only refer to the changes to the description. -- Ricardo ------------=_1649929622-12247-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 13 Apr 2022 11:21:31 +0000 Received: from localhost ([127.0.0.1]:51850 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neb3z-0000aN-8c for submit@debbugs.gnu.org; Wed, 13 Apr 2022 07:21:31 -0400 Received: from lists.gnu.org ([209.51.188.17]:44606) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neb3x-0000aF-Tj for submit@debbugs.gnu.org; Wed, 13 Apr 2022 07:21:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42654) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neb3x-0000GN-N4 for guix-patches@gnu.org; Wed, 13 Apr 2022 07:21:29 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:51701) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1neb3t-0000Oa-Gl for guix-patches@gnu.org; Wed, 13 Apr 2022 07:21:28 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 69A5F160167 for ; Wed, 13 Apr 2022 13:21:21 +0200 (CEST) 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:received:received; s=mdc; t=1649848880; x=1651663281; bh=Sf9vzwxCbO5Jj/rbqjs+b1qo/wGl0E+MdRJmWjf6k/0=; b=QlKmC+it9R00 wNq7KT0EjCtVdATACRHDi86t4srjUnXaNo0ykHC8iCrHzn+wUNMtD9vS+Ht3gMf1 bt3c77SzDs5v0+Dzf+aZqyGcIM2Aqpkqy6ABRd2A2clBp1fIBMarZGvXQ1VcdUip syN0KZRHLxUu3ktbtU1mi54cczzFrEk= 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 OjWsV8F7PC7u for ; Wed, 13 Apr 2022 13:21:20 +0200 (CEST) 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 for ; Wed, 13 Apr 2022 13:21:20 +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 15.1.2375.24; Wed, 13 Apr 2022 13:21:20 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: r-catalyst: Update to 1.18.1. 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[description]: Add Texinfo markups and clarify a sentence. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++------------ 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 803437a033..d57a09f39d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13786,14 +13786,14 @@ (define-public r-msmstests (define-public r-catalyst (package (name "r-catalyst") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi")))) + "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -13829,16 +13829,23 @@ (define-public r-catalyst "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") (description - "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass -cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as -reporters to label antibodies, thereby substantially decreasing spectral -overlap and allowing for examination of over 50 parameters at the single cell -level. While spectral overlap is significantly less pronounced in CyTOF than -flow cytometry, spillover due to detection sensitivity, isotopic impurities, -and oxide formation can impede data interpretability. We designed -CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for -preprocessing of cytometry data, including i) normalization using bead -standards, ii) single-cell deconvolution, and iii) bead-based compensation.") + "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass +cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal +isotopes rather than fluorescent tags as reporters to label antibodies, thereby +substantially decreasing spectral overlap and allowing for examination of over +50 parameters at the single cell level. While spectral overlap is +significantly less pronounced in CyTOF than flow cytometry, spillover due to +detection sensitivity, isotopic impurities, and oxide formation can impede data +interpretability. We designed @code{CATALYST} to provide a pipeline for +preprocessing of cytometry data, including: +@enumerate +@item +normalization using bead standards; +@item +single-cell deconvolution; +@item +bead-based compensation. +@end enumerate") (license license:gpl2+))) (define-public r-erma -- 2.34.0 ------------=_1649929622-12247-1--