From unknown Tue Aug 19 12:51:13 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#61220 <61220@debbugs.gnu.org> To: bug#61220 <61220@debbugs.gnu.org> Subject: Status: [patch] gnu: Add r-glad, r-italicsdata, r-pd-mapping50k-xba240, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsmooth, r-beadarraysnp and r-adacgh2. Reply-To: bug#61220 <61220@debbugs.gnu.org> Date: Tue, 19 Aug 2025 19:51:13 +0000 retitle 61220 [patch] gnu: Add r-glad, r-italicsdata, r-pd-mapping50k-xba24= 0, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsmooth, r-beadarray= snp and r-adacgh2. reassign 61220 guix-patches submitter 61220 "MadalinIonel.Patrascu@mdc-berlin.de" severity 61220 normal tag 61220 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:23:57 2023 Received: (at submit) by debbugs.gnu.org; 2 Feb 2023 02:23:57 +0000 Received: from localhost ([127.0.0.1]:60192 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPGX-0002GG-DX for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:23:57 -0500 Received: from lists.gnu.org ([209.51.188.17]:41166) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPGU-0002G8-Rm for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:23:56 -0500 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 1pNPGU-0000cY-8u for guix-patches@gnu.org; Wed, 01 Feb 2023 21:23:54 -0500 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 1pNPGR-0003Ar-TB for guix-patches@gnu.org; Wed, 01 Feb 2023 21:23:54 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= mime-version:content-type:content-type:content-language :accept-language:message-id:date:date:subject:subject:from:from :received:received; s=mdc; t=1675304602; x=1677119003; bh=Np8I2c 03qCgCSblorUlSNU/AU9hD/mJhG41iU6m6tZQ=; b=PT8AEdgdufUmXgXfuZsyDY 2XMrdPNOYN448p8gibIo1t2kR9K+FTXBHGVLRpvIYPbTt8KRibsoEkveVG+dcLE1 y42FUR5EWEdTegyePo4fFL71QQFZ9NkxVmGEjt6mTX9CoW+Vjjq4Dabi8BrmEjbB LMqWYGyQaym9F2DtRGUjc= Received: from SW-IT-P-EX3.mdc-berlin.net (mgw3.mdc-berlin.de [141.80.113.61]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id D3D89A044E for ; Thu, 2 Feb 2023 03:23:22 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) by SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.17; Thu, 2 Feb 2023 03:23:22 +0100 Received: from SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a]) by SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a%2]) with mapi id 15.01.2507.017; Thu, 2 Feb 2023 03:23:22 +0100 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "guix-patches@gnu.org" Subject: [patch] gnu: Add r-glad, r-italicsdata, r-pd-mapping50k-xba240, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsmooth, r-beadarraysnp and r-adacgh2. Thread-Topic: [patch] gnu: Add r-glad, r-italicsdata, r-pd-mapping50k-xba240, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsmooth, r-beadarraysnp and r-adacgh2. Thread-Index: AQHZNq06z72z2oYQHk6bN8dHMhPjlw== Date: Thu, 2 Feb 2023 02:23:21 +0000 Message-ID: <7175b544a6694ff09d64a005cb0cd6f1@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.51] x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27422.004 x-tm-as-result: No-10-0.091000-5.000000 x-tmase-matchedrid: I6rpFm0lrcOfkHSWeTTytMG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+tIS YzBUt2RaXVsEWVqYqaivJcrLMYkA70UuXkWTSi/R30kDaWZBE1RU4sxFq6igEUqa6TyhyXvPW4Z nuvI7TMpKKf7zZZFJTqsYZXSBnFHJCGrFz5XLS3RzmKcWXKl6quuLFZZYlisfQ6tklRJO9ihcO6 5jrNll88HMsqSrJeBmDLyAMT5IWwXVrVmL23yTxeiIWAiG856AobPQ7oVMNw+DpGjuFiRSWDWe/ rF557XfKdR/U4tRr/DYSvnsojaQCBClUEUt1OUIYDttQUGqHZU= x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10-0.091000-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27422.004 x-tm-snts-smtp: 7045FC689769B19F4EF60BCA9749CE44CE3CF5B6FB8126E42FDD16112B7538AF2002:F Content-Type: multipart/alternative; boundary="_000_7175b544a6694ff09d64a005cb0cd6f1mdcberlinde_" MIME-Version: 1.0 Received-SPF: pass client-ip=194.95.232.172; envelope-from=MadalinIonel.Patrascu@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, HTML_MESSAGE=0.001, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, TVD_SPACE_RATIO=0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) 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: -3.3 (---) --_000_7175b544a6694ff09d64a005cb0cd6f1mdcberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable * gnu/packages/bioconductor.scm (r-glad, r-italicsdata, r-pd-mapping50k-xba= 240, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsmooth, r-beadarr= aysnp and r-adacgh2): New variables. --_000_7175b544a6694ff09d64a005cb0cd6f1mdcberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

* gnu/packages/bioconductor.scm (r-glad, r-italicsdata, r-pd= -mapping50k-xba240, r-italics, r-manor, r-tilingarray, r-snapcgh, r-quantsm= ooth, r-beadarraysnp and r-adacgh2): New variables.

--_000_7175b544a6694ff09d64a005cb0cd6f1mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:22 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:22 +0000 Received: from localhost ([127.0.0.1]:60201 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJq-0002MZ-2f for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:22 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:49099) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJn-0002M2-Ml for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:20 -0500 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=1675304833; x=1677119234; bh=AJeviJTzAJoBAQb FLIn91hWVm4RYfCHn9JdpQFqUwfw=; b=TxgLmwpgG+IzQbuUGXE8+tMEMk3Gfk+ 5VrLGSfIn9wc2VAxJzRn4cs06119DOIx6EwNqKlpjCkZDX9SJUiUXVQ+7reH5+vq BMvEqusF2sa43JHj2+RIv4t+M5Yf9iwxDCVhJE687U3uTfCu7/KPXDmkRCK9UDel me+D99DRuIcM= 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 28D4B160603 for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:13 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 01/10] gnu: Add r-glad. Date: Thu, 2 Feb 2023 03:26:48 +0100 Message-ID: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10--3.713200-5.000000 X-TMASE-MatchedRID: /+von0vPuFGA/dH4BaZIKwrcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJ71Wx2uUbPLcXjfR3d0weRo4YPFy+no7QycO hvTXTlouSkIUZyUQUJ2HdNGuvvf8oo8WMkQWv6iV3LAytsQR4ewSz8fXAzKym3QfwsVk0Ubt2gy yw2xTBhUDxw8shqpvjxRxOaAn2/QF8J+/zCDiNQx6vfvGLzD3wkJhQcXmgg4dCE62TTluPracdA 6v05ZZ61BN9Vann1/Cq/+7nGbADisel4d1cuMtvjvdbOxcC5/MQtmuxiADqhvKHck16UKN1GR8A XHcOfjI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.713200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 48F257EBBCEB0EF459020791D0C65DF9A149D6165AF4B77A6CFF23D5BB0E37F82002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-glad): New variable. --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 711b988e7f..451dcfde86 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6122,6 +6122,31 @@ (define-public r-genomicranges manipulating genomic intervals and variables defined along a genome.") (license license:artistic2.0))) +(define-public r-glad + (package + (name "r-glad") + (version "2.62.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GLAD" version)) + (sha256 + (base32 + "0gb52ic5r6nkgm2ynm174vcvbmkbhhjgv71lsmxpxzcsb6rr7qj6")))) + (properties `((upstream-name . "GLAD"))) + (build-system r-build-system) + (propagated-inputs + (list gsl + r-aws)) + (native-inputs (list pkg-config)) + (home-page "http://bioinfo.curie.fr") + (synopsis "Gain and loss analysis of DNA") + (description + "This package helps with the analysis of array @acronym{CGH, comparative +genomic hybridization} data by detecting of the breakpoints in the genomic profiles +and assignment of a status (gain, normal or loss) to each chromosomal regions +identified.") + (license license:gpl2))) + (define-public r-gostats (package (name "r-gostats") base-commit: 6564a04efaf506a5ef51a7c100144fa31bbe1f31 -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:23 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:23 +0000 Received: from localhost ([127.0.0.1]:60203 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJq-0002Mn-O4 for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:23 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:57709) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJn-0002M0-Mj for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:20 -0500 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=1675304832; x=1677119233; bh=tohC5W1WH0+0H0wnJTgy+CP6lzld9rZ3eNT66MRC+gg=; b=eeyPqvUlbDEw H4JKqIajfaF8FG8d9ZgT5VC5sN6qnWaxqbJIt2UlguKuk6oW2BbvK6sg3UWp0oQJ JUwK10Sh9WCg22OJtYexXc0q7zJeMqA+p1VG24ehphn/L2EvTQnpeKd0NAZ1aJpP /Qp8iWgx3MOX3A/9f1KNEHgjzVuypsM= 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 26E271605CB for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:12 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 02/10] gnu: Add r-italicsdata. 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(license license:gpl3+))) +(define-public r-italicsdata + (package + (name "r-italicsdata") + (version "2.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ITALICSData" version 'experiment)) + (sha256 + (base32 "09d2igic3b5p7wpq98hb2lffxm1nfq9mwmnqlbdn3jv49pgz3hmw")))) + (properties `((upstream-name . "ITALICSData"))) + (build-system r-build-system) + (home-page "http://bioinfo.curie.fr") ;; no https + (synopsis "ITALICS data") + (description "Data needed to use the ITALICS package.") + (license (list license:gpl2+ license:gpl3+)))) ;; expanded from GPL + (define-public r-macrophage (package (name "r-macrophage") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:23 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:23 +0000 Received: from localhost ([127.0.0.1]:60205 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJr-0002Mw-2R for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:23 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:38693) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJo-0002M4-3r for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:20 -0500 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=1675304833; x=1677119234; bh=vfB1RlGR/vgNYLpWGZay85VqifVWQJMh/rENTBdcVuw=; b=IGJXpznKxvTG c6dzeCc2swux8vA2geUk7owd0gSv0KAB+HrfD5DHyI21qZAkzNHjvjGQeFrML4tr iCZSAFc+sca3itT4snakKgzI/DjyTUI4cfVA3nnCSDJcSgQO6mCprFor6+2Xogvn mj6Cr/jU7yLoBxrHmv5RUk3tAt9VjbY= 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 DB43C16061C for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:13 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 04/10] gnu: Add r-italics. Date: Thu, 2 Feb 2023 03:26:51 +0100 Message-ID: <20230202022657.67003-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10--2.054200-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYmDqLi3Kkph1lhGAWvOYxWo71Wx2uUbPLcXjfR3d0weRiVIhha/jkqKmA0 yITMNzjl9LQinZ4QefCP/VFuTOXUTEKa2f+1p7r3kwjHXXC/4I8prJP8FBOIaVMlrg6kQ8Tkgzp DCDJ1v2fvqJGELkFciRR2ee8FkHDh4T2hU88Wi01qDzxTxIZdLZzyWHChdtX5Gyfe8vmPIaYa8M G3sx72Qkot9h0SBLJu051Z79ST++7Bk72SZpZa8/z4Ty9JAKR/JI5vnpRHGyA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.054200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 6C296052703012B9FE656F247C310456D0399E4276893A99D6E4A78C2B57E6B42002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-italics): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fa8e60a4f4..1efafb1cd3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4510,6 +4510,33 @@ (define-public r-isoformswitchanalyzer Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") (license license:gpl2+))) +(define-public r-italics + (package + (name "r-italics") + (version "2.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ITALICS" version)) + (sha256 + (base32 "0g937h9zxkxnm424wh58b46mfasdd7pqy5c04r0a46mx9lxibgbs")))) + (properties `((upstream-name . "ITALICS"))) + (build-system r-build-system) + (propagated-inputs + (list r-affxparser + r-dbi + r-glad + r-italicsdata + r-oligo + r-oligoclasses + r-pd-mapping50k-xba240)) + (home-page "http://bioinfo.curie.fr") ;;no https + (synopsis "Normalizing of the Affymetrix GeneChip human mapping") + (description + "This package provides a method to normalize the Affymetrix GeneChip human +mapping 100K and 500K set.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. (define-public r-absfiltergsea (package -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:24 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:24 +0000 Received: from localhost ([127.0.0.1]:60207 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJs-0002N8-Fv for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:24 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:43575) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJp-0002M7-Mr for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:22 -0500 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=1675304835; x=1677119236; bh=x7Rj4BYlUECBsOz70fYLg6yWGgfDVCQV3ZZ8lKM9W3A=; b=LLPqb3w8v8Rg KCp1G7gQH/U/w4CNffxRQzhsWM3Li0g1/dn4prwGCxvQh74rVmkBfRhYXGpoKCSI NIAY2CjICFW+1GwPJ6YE0ATN7t1up4oXFh/RREhjUBkqtX54avcOgPbN7rn2WzvU O1ekZYWCSVaKiR1tFDLgljpxVGXVNGc= 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 9154C16065F for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:15 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 06/10] gnu: Add r-tilingarray. Date: Thu, 2 Feb 2023 03:26:53 +0100 Message-ID: <20230202022657.67003-6-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10--2.269400-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEA/v U1gmU80CRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9RMEg8Dnr1Idx+VvL9O1ekqbs +nJ/tFJG0SiDAofBoqSN0tVE7uH9szNgzYXdSUcZtN2GsBybzwoH9xUWW6Ss7//6LNRWr/sZ3M/ 6StC/mW5ST9wVeygStElOOOz3JPpijxYyRBa/qJcFwgTvxipFa9xS3mVzWUuAojN1lLei7RXv6l X5VNikhH8BAZ8ekpzbbrzJkbSyyQUHG1Xeby7FiV0RXAp+XvmUNKdIYtXp3n4KlgLrKWH76i4R+ iqqc8XMMRrDp03LKnlkoJqWxWZxCNZA9irUk5qtj27eUrb9iufzsdE1PQouS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.269400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 7268F267B0D8A78EDA56157011708AAE478692E7596318A273C680FF288B661A2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-tilingarray): New variable. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3339c751cb..f692114754 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -14960,6 +14960,46 @@ (define-public r-wavcluster procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) +(define-public r-tilingarray + (package + (name "r-tilingarray") + (version "1.76.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tilingArray" version)) + (sha256 + (base32 + "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd")))) + (properties `((upstream-name . "tilingArray"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-genefilter + r-pixmap + r-rcolorbrewer + r-strucchange + r-vsn)) + (home-page "https://bioconductor.org/packages/tilingArray") + (synopsis "Transcript mapping with high-density oligonucleotide tiling arrays") + (description + "The package provides functionality that can be useful for the analysis of +the high-density tiling microarray data (such as from Affymetrix genechips) or for +measuring the transcript abundance and the architecture. The main functionalities +of the package are: +@enumerate +@item the class segmentation for representing partitionings of a linear series of +data; +@item the function segment for fitting piecewise constant models using a dynamic +programming algorithm that is both fast and exact; +@item the function confint for calculating confidence intervals using the strucchange +package; +@item the function plotAlongChrom for generating pretty plots; +@item the function normalizeByReference for probe-sequence dependent response +adjustment from a (set of) reference hybridizations. +@end enumerate") + (license license:artistic2.0))) + (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:25 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:25 +0000 Received: from localhost ([127.0.0.1]:60209 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJs-0002NB-St for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:25 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:50093) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJo-0002M5-UM for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:22 -0500 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=1675304834; x=1677119235; bh=UFwuyBwENReeo4JvYw4PbSTIdfDqprO851k3rlEAT54=; b=AGyDdKlLa1ki 5c1K03SVCK98io+rW0NddaHJY0R8LTIoW93MeY5jLRb7SxbrWuvcety8OErkdWWy eBgojKU9BbNN/3npDEvlRgsfQtiSu/HMfFUD7p5TAjGF5w8otcOV8wxU8Nk/xskq iBtg499OU5EJ7d6idGCa6rzYYJz+Qn0= 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 BC74F160630 for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:14 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 03/10] gnu: Add r-pd-mapping50k-xba240. Date: Thu, 2 Feb 2023 03:26:50 +0100 Message-ID: <20230202022657.67003-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10-1.393600-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkELI5 /dPWFNfzRRa406V/YwyBUGewL2YXt8i5BCxh8k4DwLYk+NSxc5r4qCLIu0mtIOPsX9qV3ark7zu b46SCOG6hxWAM2J2vYBf6uqcdjTP5OpgF210IR5rdCok3ibXlQeuLFZZYlisfHxPMjOKY7A+u65 UDD0aDgsRB0bsfrpPI34T9cYMsdwx9pkL/lRJGPPi18QuPzYkqJjFTcuOKs5FLhJ+yfcG1b3mwO kVA6aqoz0sVw1+qnJNPDFfVge4SeawnrlCVeGXI+9ExW9vXP27cUke23u350xU7OJY7bdPeD9iv /sJMsVc7Oyi/ulxQeKUgZdIaXg4f X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.393600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 691B77956355292CCBEA6D9F79B585D56814624C66020BD1FD0D206F563E0C782002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-pd-mapping50k-xba240): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed08807f07..fa8e60a4f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -115,6 +115,32 @@ (define-public r-org-bt-eg-db based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) +(define-public r-pd-mapping50k-xba240 + (package + (name "r-pd-mapping50k-xba240") + (version "3.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pd.mapping50k.xba240" version + 'annotation)) + (sha256 + (base32 "1a1f3lh5ywhyjawdbj2fzban85c8jz70lfcv3pagd5piincjwxq8")))) + (properties `((upstream-name . "pd.mapping50k.xba240"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-dbi + r-iranges + r-oligo + r-oligoclasses + r-rsqlite + r-s4vectors)) + (home-page "https://bioconductor.org/packages/pd.mapping50k.xba240") + (synopsis "Platform design info for Affymetrix Mapping50K_Xba240") + (description "This package provides annotations for pd.mapping50k.xba240.") + (license license:artistic2.0))) + (define-public r-reactome-db (package (name "r-reactome-db") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:27 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:27 +0000 Received: from localhost ([127.0.0.1]:60216 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJv-0002Nr-84 for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:27 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:54207) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJt-0002MO-Mx for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:26 -0500 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=1675304836; x=1677119237; bh=mwTqzUWQtzNd1SaAC4mvsQiouumUt+2B6SKLIV0DRlI=; b=MUzJmEuyQ58r m8ocExXWRxfO1r7wASU7MhhEKiMwPZFGdu3FQtVSKXx+WGzztdVg5vVg7cURHiYH 83R2JARdtoGvmazN8kogbJo3TFJUOQitxuIS8vaZGPREJuY4/ySWag1ZIvoxNF/R TnRC2umCIIW5bSz8Sw1zXjbQshDlths= 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 55F8216066A for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:16 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 07/10] gnu: Add r-snapcgh. Date: Thu, 2 Feb 2023 03:26:54 +0100 Message-ID: <20230202022657.67003-7-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10--2.090600-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEPd3 mOo2koGARRa406V/YwyBUGewL2YXt4x1g1lTiexdwLYk+NSxc5r4qCLIu0mtIOpHSOTZIqcMqbs +nJ/tFJHjocCYVeB3TwAWNF4h7aVC1pVckLHgk0Krm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu3aDLLDbFMGFHAlUn1pyOdBfdtLDSBFHsE0ADsLE+C8PXXp0pZ1eh0fI32x+eT/IByqcp 3OF0d3VSUJhhSIPiLd0KzFKMyYxFiiOUsrx4M6hx6Xh3Vy4y2+O91s7FwLn8xC2a7GIAOqG8ody TXpQo3UZHwBcdw5+Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.090600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 7299C102918881D5DBA7F8D58A4D8E0E2A635B37022431148980477F137368612002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-snapcgh): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f692114754..bce8319dcb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18185,6 +18185,33 @@ (define-public r-pathview large-scale and fully automated analysis.") (license license:gpl3+))) +(define-public r-snapcgh + (package + (name "r-snapcgh") + (version "1.68.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "snapCGH" version)) + (sha256 + (base32 + "1zxvl8mkby7yb5kppddag6k9w78d1fm6adx52h4cgrfckn28w64q")))) + (properties `((upstream-name . "snapCGH"))) + (build-system r-build-system) + (propagated-inputs + (list r-acgh + r-cluster + r-dnacopy + r-glad + r-limma + r-tilingarray)) + (home-page "https://bioconductor.org/packages/snapCGH") + (synopsis "Segmentation, normalisation and processing of the aCGH data") + (description + "This package provides methods for segmenting, normalising and processing +aCGH data. snapCGH also includes plotting functions for visualising raw and +segmented data for individual and multiple arrays.") + (license (list license:gpl2+ license:gpl3+)))) ;; expanded from GPL + (define-public r-snpstats (package (name "r-snpstats") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:28 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:28 +0000 Received: from localhost ([127.0.0.1]:60218 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJv-0002Nv-KW for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:28 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:58671) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJt-0002MP-NI for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:26 -0500 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=1675304837; x=1677119238; bh=Gv81YdwKSbu+bhP05cfVMLJprTOjO9ZUgw7cZck+614=; b=eJ8tBXNp43ja ohZFGaej6Ph5UChkZnI1IJLMU9/KzueWfEfYyc9hzIM3LRgpEKheYgPEU10sKeIh gG3rPmoQGRRgyXsVipV45VAyysKvE3kGyPA83niX208hmR2h0Yl++EYHLEJkprq6 ui6v306aZCzvQ9MT5x/TnTmp+2FUvO8= 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 12EFC1606AA for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:17 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 08/10] gnu: Add r-quantsmooth. Date: Thu, 2 Feb 2023 03:26:55 +0100 Message-ID: <20230202022657.67003-8-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10--1.043800-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkENA3 SZ3aWimvnMBQUHFOVS/uNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHOSL mthZG++aS9TBaifEV6fgtOgp2d5rv+DGmV2RMPUIU7OE9fcKa8aCDl9vXDTLXgSsbX1LRNK2YDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07ba607moR85Rjr+1pFkLq9h6iEk6WgoxwQvXX Mx3+ivg1s+1Bsl4kY18KBjiMKQxpmYPAglvi9f2Taqfl33JzaLQ59nw4RyHh6OL50Z2t+FPdAnz xkc/wOO+Yl/q6i1mnv1mO1iYLJDqT4cbBIKMuHq+68HqACCvKA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.043800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: D4D5018E87A578B51A05C6B91AE68B7230071311CBFC3879029078FCA29311EB2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-quantsmooth): New variable. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bce8319dcb..07207ebc38 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8738,6 +8738,33 @@ (define-public r-oligo Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (license license:lgpl2.0+))) +(define-public r-quantsmooth + (package + (name "r-quantsmooth") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "quantsmooth" version)) + (sha256 + (base32 "1adwws3brb01d4g6yidipnd8akkiyc3gpdr876hy57qnmcq8xipp")))) + (properties `((upstream-name . "quantsmooth"))) + (build-system r-build-system) + (propagated-inputs (list r-quantreg)) + (home-page "https://bioconductor.org/packages/quantsmooth") + (synopsis "Quantile smoothing and genomic visualization of array data") + (description + "This package implements quantile smoothing. It contains a dataset used to +produce human chromosomal ideograms for plotting purposes and a collection of +arrays that contains data of chromosome 14 of 3 colorectal tumors. The package +provides functions for painting chromosomal icons, chromosme or chromosomal +idiogram and other types of plots. Quantsmooth offers options like converting +chromosomal ids to their numeric form, retrieving the human chromosomal length +from NCBI data, retrieving regions of interest in a vector of intensities using +quantile smoothing, determining cytoband position based on the location of the +probe, and other useful tools.") + (license license:gpl2))) + (define-public r-qvalue (package (name "r-qvalue") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:28 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:28 +0000 Received: from localhost ([127.0.0.1]:60220 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJw-0002O2-21 for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:28 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:46089) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJt-0002MQ-Nl for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:26 -0500 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=1675304837; x=1677119238; bh=H9wTYpTp2GeWztBtaQjhv7Cnl9V0yc0j0BnjQ5E2jvw=; b=KPtTUXv4b/X7 1dh/wP6Zu3T8Xzrw+Eg392tbC/3eMdpixomlwvKZHnxjy34eLt0pNkGPyAZaL42e x3BuLQPVQLHSYqvGSJJLmljx4CEG5WI3Oi+Y4VGiu3nDP1h1FfHdjZGK/UZKa/ee ux/IszK28nljsuq7nQ1eafbqEyx9+60= 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 D1C951606B6 for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:17 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 09/10] gnu: Add r-beadarraysnp. Date: Thu, 2 Feb 2023 03:26:56 +0100 Message-ID: <20230202022657.67003-9-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10-0.740400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6HlDQRrnQLaUXjfR3d0weRtodkNYFbOrOvqA Jrx96r11yf070dvqMr0t6NL8M7oHYb6wZx1ul0pw8xwCU4LSqsAseQVcTRnF2lwV2iaAfSWcURS Scn+QSXmVV1G+Ck2l7+gtHj7OwNO22utO5qEfOUdxkmk6txqjt2gT+QK371ItOXVqyfFDszCqza ehs+PGzCdrWYFwUZzQokAkCDRkWQ6Qy/TwOziEdzbkkltTuhO3dxXpyzvPkUHQJ88ZHP8DjvmJf 6uotZp79ZjtYmCyQ6k+HGwSCjLh6vuvB6gAgryg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.740400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: B7150F323F58ABC6C600E320FC57F5AD85256772F766AD4AB04A34BCF66BB0ED2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-beadarraysnp): New variable. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 07207ebc38..c509dffb4c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17081,6 +17081,26 @@ (define-public r-beachmat matrices.") (license license:gpl3))) +(define-public r-beadarraysnp + (package + (name "r-beadarraysnp") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beadarraySNP" version)) + (sha256 + (base32 "06hy89pclbyxjw5yf5i9bc3wr789b9pmhd9sdchgljlijs9vcj6g")))) + (properties `((upstream-name . "beadarraySNP"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-quantsmooth)) + (home-page "https://bioconductor.org/packages/beadarraySNP") + (synopsis "Normalization and reporting of Illumina SNP bead arrays") + (description + "This package is importing data from Illumina SNP experiments and it performs +copy number calculations and reports.") + (license license:gpl2))) + ;; This package includes files that have been taken from kentutils. Some ;; parts of kentutils are not released under a free license, but this package ;; only uses files that are also found in the free parts of kentutils. -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:28 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:28 +0000 Received: from localhost ([127.0.0.1]:60222 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJw-0002OA-DJ for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:28 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:40265) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJu-0002MX-4K for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:26 -0500 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=1675304839; x=1677119240; bh=CoEhEJlpDBlvGSY6wk13bQenZUKt5+ys51S91Wu4KPM=; b=B0OhGEpsAtUv IwvJkqZfeiA86OHlKbo2UunLs/yebfhBzGAhn40ApP4Edjj1hRFrzDo0sljIgaOs 9/jmoVYomkgO+sZxefXXNEcuI0FV2bq9XVCqdwhHZPzdkaN0wdG2P5XQIxKcJQlc 5otCucDSEBn1e+hgpKhNwe1Z8ZEv6mQ= 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 8A4891606E0 for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:19 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 05/10] gnu: Add r-manor. Date: Thu, 2 Feb 2023 03:26:52 +0100 Message-ID: <20230202022657.67003-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10--0.760400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJM63WD5CqqQDQrcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFDzLIHIzVyU2TuNT8xdcEnQwE+dA3RWUSvj5hLPCX3ZdOFzNNPDc6umGmj1qXcLu1ioYv KPGlaNfEevfN9eU+/vv/jG5sJvhKorWL/xQJnm46rm7DrUlmNkIAy6p60ZV62yA7duzCw6dIBpR CTkRk5SfoLR4+zsDTttrrTuahHzlEb7puurRRG3vsgw1fkyPWGZx+kpNAcjee7ikXW21lbVUatS rNDTdH9n7KEHck0ql49QG1QW3rZ8oBm3HaqfqLuQnwkUtP3AEh0CfPGRz/A475iX+rqLWae/WY7 WJgskOpPhxsEgoy4er7rweoAIK8o X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.760400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: CD697A1DAFC78CC293006402E33A9F9A8D3FD225C1BA8CFBC79AC6E04C0B0B782002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-manor): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1efafb1cd3..3339c751cb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6518,6 +6518,29 @@ (define-public r-makecdfenv package that automatically loads that environment.") (license license:gpl2+))) +(define-public r-manor + (package + (name "r-manor") + (version "1.70.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MANOR" version)) + (sha256 + (base32 "16b30bmyzml97cjdbh6h9ky5c4h5ws2a3g2xkxnd55sd3jg64jgx")))) + (properties `((upstream-name . "MANOR"))) + (build-system r-build-system) + (propagated-inputs (list r-glad)) + (native-inputs (list r-knitr)) + (home-page "http://bioinfo.curie.fr/projects/manor/index.html") ;;no https + (synopsis "CGH micro-array normalization") + (description + "This package ofers functions for importation, normalization, visualization, +and quality control to correct identified sources of variability in array of +@acronym{CGH, comparative genomic hybridization} experiments.") + (license license:gpl2))) + + (define-public r-maser (package (name "r-maser") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Feb 01 21:27:29 2023 Received: (at 61220) by debbugs.gnu.org; 2 Feb 2023 02:27:29 +0000 Received: from localhost ([127.0.0.1]:60224 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJw-0002OH-R1 for submit@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:29 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:42459) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pNPJt-0002MR-OZ for 61220@debbugs.gnu.org; Wed, 01 Feb 2023 21:27:27 -0500 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=1675304838; x=1677119239; bh=keD1tGsNedgKxXPAr6iHAvBwBqmpEnJA+vouOHkK97k=; b=D3FZxP0f+3py AmsXMhm+YSUjlj8GtM25/l8SAjRBI6xVTiZciMeapE2YkJGZSXAr+vfsY2wEf4Ox zgnp9Jt2TDQIt44aB9oLLTF5W8PiqCqJpT53SY1qpu4Vl2XVggHREKC3XzM3sjnR 0MQnX+gmzUryC+uUix8Nj23bbnUmMVU= 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 88E771606CA for <61220@debbugs.gnu.org>; Thu, 2 Feb 2023 03:27:18 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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 15.1.2507.17; Thu, 2 Feb 2023 03:27:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61220@debbugs.gnu.org> Subject: [PATCH 10/10] gnu: Add r-adacgh2. Date: Thu, 2 Feb 2023 03:26:57 +0100 Message-ID: <20230202022657.67003-10-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-AS-Result: No-10-0.214800-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEDlU lx4PIvA7cKOSpdxu/RvR2Jk3kswrWCq+GZ9ZHxIhuW77/y896sj4uJ1REX4MHaMZvngJnzipCMm WJ6tUT+eJek9VNKq6xVhJV8dlFHDML/fdNahJQfrX3j/lf1V8LBqZh28Q6E3rU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DL4+xFM37BUAINFGJVQaEaZ3+Cg2kxpAnXaru kmaNdZXqRZMiwqrIw290LZdnSs2p5Ep7cOTgjnF/yInuOzz8H/MmDWh9xmF49xSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.214800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27422.004 X-TM-SNTS-SMTP: 30E8593F405BFCE441527E26D8F557D85D56E1A2B99C4583E4DF57B443CFDC602002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61220 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-adacgh2): New variable. --- gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c509dffb4c..b351936cd8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -31,6 +31,7 @@ (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -1800,6 +1801,49 @@ (define-public r-absseq ranking by fold-change and visualization.") (license license:gpl3+))) +(define-public r-adacgh2 + (package + (name "r-adacgh2") + (version "2.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ADaCGH2" version)) + (sha256 + (base32 "0g9x3lnr56035wq9ijdcri4sz5pwj8184yxm415gmsxrii9xvpfd")))) + (properties `((upstream-name . "ADaCGH2"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'set-PYTHONPATH + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" + (getenv "GUIX_PYTHONPATH")))))))) + ;; This is needed by toMap.py script which is not compatible with python3 + (inputs (list python2-minimal)) + (propagated-inputs + (list r-acgh + r-bit + r-cluster + r-dnacopy + r-ff + r-glad + r-snapcgh + r-tilingarray + r-waveslim)) + (home-page "https://github.com/rdiaz02/adacgh2") + (synopsis "Big data analysis from aCGH experiments") + (description + "This package analysis and creates plotts of array @acronym{CGH, comparative +genomic hybridization} data. Also, it allows usage of @acronym{CBS, Circular +Binary Segementation}, wavelet-based smoothing, HMM, BioHMM, GLAD, CGHseg. Most +computations are parallelized (either via forking or with clusters, including MPI +and sockets clusters) and use ff for storing data.") + (license license:gpl3+))) + (define-public r-adam (package (name "r-adam") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Feb 07 04:31:45 2023 Received: (at 61220) by debbugs.gnu.org; 7 Feb 2023 09:31:45 +0000 Received: from localhost ([127.0.0.1]:51102 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pPKKH-0007U8-E2 for submit@debbugs.gnu.org; Tue, 07 Feb 2023 04:31:45 -0500 Received: from sender3-of-o59.zoho.com ([136.143.184.59]:21986) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pPKKF-0007Tv-61; Tue, 07 Feb 2023 04:31:44 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1675762298; cv=none; d=zohomail.com; s=zohoarc; b=JdzAMtQFCkrI4m2/OFeX5UsLUARgex5NRcs5Ureo7mHMg+CZUuVLFaL378MjzuoqGW0yAuoQqoun+/Ii3B+K7P+zghYOij7VnZMa5ww0LE2g+fyOC4/IfNIw73gha2WWiHJkKnqdR9iXZNgKBLHbRzSA2yJ7denyJeDUjnga2xQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1675762298; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=zqlLX6BgIYdr8u4Fu2kKTUiuWAltsBS3xBTHWlZNcDc=; b=Y1cdhuPlBKBKrT4nmdlB2Ocad6hN0AnxNYpi2XA6c7pSeT6K986AJtSiC+TE6ourTEIpBR+o0gcFwo/QkCIwevzEwl9/IS0XvhemP6K0A09elQDwuJPUx5s240dNNSlpS1b62wNyffn4S319Whhp9welD/LJSAYxO9urI5hcJ9U= 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=1675762298; 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=zqlLX6BgIYdr8u4Fu2kKTUiuWAltsBS3xBTHWlZNcDc=; b=V9GaWVCCL4rWYFzbAoP1c/Z6Spj2REE4fgh+TraTlvuWjzmw9TXuZMg6B4Ch2PF7 77dYeb/AoimRbIoB/UleLodxjk0VsVvCuj7+2w49Gw2cGyCumNveOhhQX1LDj4Rz1i/ 2cUYq5ReWxzkqasc54gjSTY4sMKz6soMQyj5gMGg= Received: from localhost (58-110-142-46.pool.kielnet.net [46.142.110.58]) by mx.zohomail.com with SMTPS id 1675762295791746.2479744177563; Tue, 7 Feb 2023 01:31:35 -0800 (PST) References: <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> <20230202022657.67003-10-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61220] [PATCH 10/10] gnu: Add r-adacgh2. Date: Tue, 07 Feb 2023 10:30:23 +0100 In-reply-to: <20230202022657.67003-10-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: <87y1p96cuj.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: 61220 Cc: debbugs-submit@debbugs.gnu.org, 61220@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-adacgh2): New variable. [=E2=80=A6] > (define-module (gnu packages bioconductor) > #:use-module ((guix licenses) #:prefix license:) > + #:use-module (guix gexp) [=E2=80=A6] > + (arguments > + (list > + #:phases > + #~(modify-phases %standard-phases > + (add-before 'configure 'set-PYTHONPATH > + (lambda _ > + (setenv "PYTHONPATH" > + (string-append (getcwd) ":" > + (getenv "GUIX_PYTHONPATH")))))))) This phase seems unnecessary. > + ;; This is needed by toMap.py script which is not compatible with py= thon3 > + (inputs (list python2-minimal)) The only reason for Python 2 is the outdated =E2=80=9Cprint=E2=80=9D, which= is not called as a function but used as a statement. I patched it instead. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Tue Feb 07 04:33:19 2023 Received: (at 61220-done) by debbugs.gnu.org; 7 Feb 2023 09:33:19 +0000 Received: from localhost ([127.0.0.1]:51108 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pPKLn-0007Ww-6K for submit@debbugs.gnu.org; Tue, 07 Feb 2023 04:33:19 -0500 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21737) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pPKLl-0007Wk-5c for 61220-done@debbugs.gnu.org; Tue, 07 Feb 2023 04:33:17 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1675762395; cv=none; d=zohomail.com; s=zohoarc; b=lM39QKrodPjK87CAJuFqI9EuOJaTMcpfOxokffkWrkAjl0L/29kJfTS+MkNdWoUTUslDMQWTDxdJ1tZ+OCkP8mbxS2uQs49xzdGEjUW0DzU13rGhjxzvCE6bV5p46CreNaAEFo8mwFVwA80w/lO5i/Rwj96lF4w6d/sembTqags= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1675762395; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=a9DAab1VLlg7A6bj/gpGp86CQU/NxU+WbL93WgCITnc=; b=nSZtJsHSAif+AbAP7FHXa/JoV5JB9Wj8IezTutdqmN7S+5jJJZw0+Jzi0Egh9wqd7ADr05SQoZ3GvQ4zGtMKigcsRstg02iwxEaZx9sXVSPmM0ZYEL5rIhOiw04UQudz6FtaF7eZDSJh+n6vnlnMMoz6/LFnxn+qAdPYpGQzsvM= 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=1675762395; 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=a9DAab1VLlg7A6bj/gpGp86CQU/NxU+WbL93WgCITnc=; b=QZufP/R/9EYR0Z235cun+JmuBrA9FCWSwhk3lIK0ZoCLv0Rmp5nABoeX49NSY3fk zpFGsB3XCOer2YxLrlt6uJZJbgZ6YWis4pE+hfJOEhwoSTDBNTRtOxWBQk7CKw6UKyV IN7IKrBW66t4z8gzGR0N132DSkuGuoM7hg/1b7Xs= Received: from localhost (58-110-142-46.pool.kielnet.net [46.142.110.58]) by mx.zohomail.com with SMTPS id 1675762394462987.9394426736059; Tue, 7 Feb 2023 01:33:14 -0800 (PST) References: <7175b544a6694ff09d64a005cb0cd6f1@mdc-berlin.de> <20230202022657.67003-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61220] [PATCH 01/10] gnu: Add r-glad. Date: Tue, 07 Feb 2023 10:31:46 +0100 In-reply-to: <20230202022657.67003-1-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: <87ttzx6crs.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: 61220-done Cc: 61220-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-glad): New variable. [=E2=80=A6] Thanks for this patch series. I applied them all after changes to the description of almost all packages, and changes to the line comments. I also moved gsl from propagated-inputs to inputs. --=20 Ricardo From unknown Tue Aug 19 12:51:13 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 07 Mar 2023 12:24:07 +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