From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 05 10:19:18 2022 Received: (at submit) by debbugs.gnu.org; 5 Dec 2022 15:19:18 +0000 Received: from localhost ([127.0.0.1]:36642 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DFW-0004J7-GD for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:19:18 -0500 Received: from lists.gnu.org ([209.51.188.17]:55978) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DFU-0004J1-Ns for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:19:17 -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 1p2DFT-0003IZ-AY for guix-patches@gnu.org; Mon, 05 Dec 2022 10:19:16 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p2DFP-0008Go-LC for guix-patches@gnu.org; Mon, 05 Dec 2022 10:19:15 -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=1670253530; x=1672067931; bh=BA59Cc P8BKZvEs/PvM233UEwAHk3A0HUyb9dvbfcMmM=; b=fL/JWGWVlAo2RsRG2g2YBQ qpREc7kY1qI6jBIlE3DZc5PxSCWTBJzfuk7o6DuvsGSUf7VFkT9ZmdQeLpIgV/kW vnJTrA3K8mdG4QYi9JjayUhikEH886bWzfsPzQ7s68VdEJouEHVQbLOxeSOSdOFX Oh80EbS25Fdue8T5tv5q0= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id B5F71160A2A for ; Mon, 5 Dec 2022 16:18:50 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) 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 15.1.2507.16; Mon, 5 Dec 2022 16:18:50 +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 15.01.2507.016; Mon, 5 Dec 2022 16:18:50 +0100 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "guix-patches@gnu.org" Subject: [PATCH] gnu: Add r-makecdfenv, r-altcdfenvs and r-harshlight. Thread-Topic: [PATCH] gnu: Add r-makecdfenv, r-altcdfenvs and r-harshlight. Thread-Index: AQHZCLx9DCe5gcC/A0uiH28F8ol+Jg== Date: Mon, 5 Dec 2022 15:18:49 +0000 Message-ID: <7734e3c0299847c9a5c367e2bcf77a6a@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-14.0.0.3092-9.0.1002-27306.001 x-tm-as-result: No-10-0.545300-5.000000 x-tmase-matchedrid: I6rpFm0lrcOfkHSWeTTytMG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+tIS YzBUt2RaXVsEWVqYqaivJcrLMYkA70UuXkWTSi/R30kDaWZBE1RU4sxFq6igEUqa6TyhyXvPW4Z nuvI7TMrDwzy9+7FiZKdM4dMtu0jXYs5b7O/X32Srm7DrUlmNkH8mA3sDDq0Ab0etregGn/1vHi Dsvwe8+K8WWRHWX8WV5Nup7jAEGIbKXviWNfxCdOwUTtQAreVvoCZ3N5mmRP4QO8BwZ/7KrjyV3 D5IMRMJm2C2cLnXbN+PaW6Ua24rHSDFuFEiHCqrftwZ3X11IV0= x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10-0.545300-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27306.001 x-tm-snts-smtp: 93A624E0C6CEDD29796E93BFAD3FB8A9364D432C0A63254347DEAD2C2F36F4E92002:F Content-Type: multipart/alternative; boundary="_000_7734e3c0299847c9a5c367e2bcf77a6amdcberlinde_" MIME-Version: 1.0 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, HTML_MESSAGE=0.001, 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: -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 (--) --_000_7734e3c0299847c9a5c367e2bcf77a6amdcberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable * gnu/packages/bioconductor.scm (r-makecdfenv, r-altcdfenvs and r-harshligh= t): New variables. --_000_7734e3c0299847c9a5c367e2bcf77a6amdcberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

* gnu/packages/bioconductor.scm (r-makecdfenv= , r-altcdfenvs and r-harshlight): New variables.

--_000_7734e3c0299847c9a5c367e2bcf77a6amdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 05 10:22:14 2022 Received: (at 59835) by debbugs.gnu.org; 5 Dec 2022 15:22:14 +0000 Received: from localhost ([127.0.0.1]:36660 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIM-0004LR-1u for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:14 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:35921) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIK-0004L9-Bg for 59835@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:12 -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=1670253726; x=1672068127; bh=h526KI0Kc2zgOdxwY+yPqegNVPb8kqXeqqYn9UFfiUs=; b=Kms4+RPhett3 qLQZSjjDUfS6/C6IxDhoCFtF0JVONRiWa//nsWtDlYy7S5cjlvXL6vn4I6iEAxnm Eip6D0XRqvoxUlyx+ADFC2rxwqCSEK9NdoqZWtXnIAeMOaPnNFmWRK0fEUwgUgjv zEvr0xFkakiQ+BlgJYSQDkaZMB6Yp8U= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 216B2A0B2D for <59835@debbugs.gnu.org>; Mon, 5 Dec 2022 16:22:06 +0100 (CET) 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 15.1.2507.16; Mon, 5 Dec 2022 16:22:04 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <59835@debbugs.gnu.org> Subject: [PATCH 2/3] gnu: Add r-altcdfenvs. Date: Mon, 5 Dec 2022 16:21:52 +0100 Message-ID: <20221205152153.18545-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> References: <20221205152153.18545-1-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: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-AS-Result: No-10--3.419400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCx4SsGg2DQOYulFgQZ3zLO36eM /cGSFB1LMU8NOk/D5DbtCCJ8Cv8fxjzv7niIkhlfG+nS24MzHeQseQVcTRnF2lwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYUms9rk+YQkcP4CNhPfjljQnjLazFKhX1mRzCofM6icDnRR5 J68wva3EhW1t0FRC7zDF0A9jQ1s1lAVvC16ciJLPpjDNy/updHHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.419400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-SNTS-SMTP: 257C4DB7866E913F765BC9CD238E247B4FF83AAB5DA767262AF9F7BE5796B6D32002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 59835 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-altcdfenvs): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7cace3317c..37b84983c4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2492,6 +2492,37 @@ (define-public r-alpine data.") (license license:gpl2+))) +(define-public r-altcdfenvs + (package + (name "r-altcdfenvs") + (version "2.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "altcdfenvs" version)) + (sha256 + (base32 + "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0")))) + (properties `((upstream-name . "altcdfenvs"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-biocgenerics + r-biostrings + r-hypergraph + r-makecdfenv + r-s4vectors)) + (home-page "https://bioconductor.org/packages/altcdfenvs") + (synopsis + "Convenience data structures and functions to handle CDF environments") + (description + "The package is usable with @code{Affymetrix GeneChip} short oligonucleotide +arrays, and it can be adapted or extended to other platforms. It is able to +modify or replace the grouping of probes in the probe sets. Also, the package +contains simple functions to read @code{R} connections in the @code{FASTA} format +and it can create an alternative mapping from sequences.") + (license license:gpl2+))) + (define-public r-aneufinder (package (name "r-aneufinder") -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 05 10:22:14 2022 Received: (at 59835) by debbugs.gnu.org; 5 Dec 2022 15:22:14 +0000 Received: from localhost ([127.0.0.1]:36662 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIM-0004LT-Fc for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:14 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:60153) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIK-0004L8-Bf for 59835@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:13 -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=1670253725; x=1672068126; bh=2Puufp+L6+SO27x rQvkoQql0CGX2xuuKIn3N90mhXdY=; b=kUN76sFZF6vythzv9ArNuaPyKMHnhNQ y+6oXdFsadvInkWWbY2P1Pm5wA0+NcZjobAeXUF2YKtYjeDp9ecF/PraVQwH4Qqw VkJO8q1U4UAkeYfQSN86Vi2q0XluiVkSwcPUWNUBqhJHcqKbOwW8WtT0DMZbB5XH Cslq6j46x3ZM= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 538D9A0B25 for <59835@debbugs.gnu.org>; Mon, 5 Dec 2022 16:22:05 +0100 (CET) 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 15.1.2507.16; Mon, 5 Dec 2022 16:22:04 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <59835@debbugs.gnu.org> Subject: [PATCH 1/3] gnu: Add r-makecdfenv. Date: Mon, 5 Dec 2022 16:21:51 +0100 Message-ID: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 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-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-AS-Result: No-10--2.389000-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCzrr41gyMH26/v4Y1Mygj090zl xXfg8EXkMpd+A7BXtAA1ArEwC9IavygR7McnOqmXGL//8mlodA0LixrsCJ1jTlCkt7JatNPWeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DGrtcW2vkbkgQ9p72ozF1myE1TN3d73EecSlr 7l4W88yDxUUAO+vgjbtXvKFscnfl4E8He1zaK+jbbPkZG2OgMMW8VxiLyb1RNxSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.389000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-SNTS-SMTP: 1BDD3B5C8BA3F798CAE97FA0EA8B3DB8009C8F8D5C4C9AEC0477C4FA33ECB0072002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 59835 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-makecdfenv): 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 c62c5970b8..7cace3317c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6010,6 +6010,33 @@ (define-public r-made4 datasets (coinertia analysis).") (license license:artistic2.0))) +(define-public r-makecdfenv + (package + (name "r-makecdfenv") + (version "1.74.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "makecdfenv" version)) + (sha256 + (base32 + "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25")))) + (properties `((upstream-name . "makecdfenv"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs + (list r-affy + r-affyio + r-biobase + r-zlibbioc)) + (home-page "https://bioconductor.org/packages/makecdfenv") + (synopsis "Chip description file environment maker") + (description + "This package implements two functions. One of them reads an @code{Affymetrix} +@acronym{CDF, chip description file} and creates a hash table environment containing +the location/probe set membership mapping. The other one creates a package that +automatically loads that environment.") + (license license:gpl2+))) + (define-public r-metaneighbor (package (name "r-metaneighbor") base-commit: b2a848d23d37f31496e1ff664f1dcf6abcdcc388 -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 05 10:22:15 2022 Received: (at 59835) by debbugs.gnu.org; 5 Dec 2022 15:22:15 +0000 Received: from localhost ([127.0.0.1]:36664 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIM-0004La-Pv for submit@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:15 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:57221) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p2DIL-0004LA-0Q for 59835@debbugs.gnu.org; Mon, 05 Dec 2022 10:22:13 -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=1670253726; x=1672068127; bh=WXzgi3q8bdlg9C6E5G1jBtYDaLoF8/P4ZpGsyxd0UvI=; b=TAHAllevvzBl VCLrQ2Y4+/7u6D89yFbAVfpmsrF6/Zvt5CZALYCQlekCZ6m2xhcjdbfz1Vlw1iWh a9kES1/KDuOVxoo08JxTKvUYwBoH7OsCQ6Eu/Y5rybBcv5VhyI7P+zpGsYxj0ORX HiiiCPP7EangkxGhS6131d4P34WygOo= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id D3EE6A0B31 for <59835@debbugs.gnu.org>; Mon, 5 Dec 2022 16:22:06 +0100 (CET) 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 15.1.2507.16; Mon, 5 Dec 2022 16:22:04 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <59835@debbugs.gnu.org> Subject: [PATCH 3/3] gnu: Add r-harshlight. Date: Mon, 5 Dec 2022 16:21:53 +0100 Message-ID: <20221205152153.18545-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> References: <20221205152153.18545-1-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: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-AS-Result: No-10--0.889200-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90Badv+F8ucSI194/5X9VfCwDhJZ+MB6jvEXjiYP9VKZ993G Y7dNTJ6iI0Ejneva935soi2XrUn/JQYMORuDWAmTfaY87m2dqx8K21zBg2KlfB00/kkeBTwDOct sNf11NFmPrcA4Ba/vN+L7erCxu0i2waTZnVONey9XL378m98lLIQ+dyi4hJiVQmC2dDa5gXh2rC gKe7bbpU5jmVBSXVrQoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.889200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27306.001 X-TM-SNTS-SMTP: 5E26776C86BADE76E9A3F1CB9BFA5DA15ACE432AA78D5D070E4BBE9FBB3FD0B72002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 59835 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-harshlight): 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 37b84983c4..346fccfd3a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5854,6 +5854,33 @@ (define-public r-gseabase Enrichment Analysis} (GSEA).") (license license:artistic2.0))) +(define-public r-harshlight + (package + (name "r-harshlight") + (version "1.70.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Harshlight" version)) + (sha256 + (base32 + "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm")))) + (properties `((upstream-name . "Harshlight"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-altcdfenvs + r-biobase)) + (home-page "http://asterion.rockefeller.edu/Harshlight/") + (synopsis "Corrective make-up program for microarray chips") + (description + "The package detects extended diffuse and compact blemishes on microarray +chips. @code{Harshlight} marks the areas in a collection of chips (affybatch +objects). A corrected @code{AffyBatch} object will result. The package replaces +the defected areas with N/As or the median of the values of the same probe. The +new version handles the substitute value as a whole matrix to solve the memory +problem.") + (license license:gpl2+))) + (define-public r-hpar (package (name "r-hpar") -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 12 09:36:56 2022 Received: (at 59835-done) by debbugs.gnu.org; 12 Dec 2022 14:36:56 +0000 Received: from localhost ([127.0.0.1]:53370 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jvM-0007ct-H8 for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:36:56 -0500 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21809) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jvK-0007cf-JY for 59835-done@debbugs.gnu.org; Mon, 12 Dec 2022 09:36:55 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855812; cv=none; d=zohomail.com; s=zohoarc; b=hqIJkhI3tdAZcqsZegQJlv5RhxhAhvUJihM8P16Y69nZ091vCCK/GiuHlvvTBgyE4jB6YoItYWkr+AcDiIebqt7PXSR1o9Y2+ssHPGCa9h5iRxG09ReoVEgkRNKfdQX3E6kfWOc5BPjJUtTYmh56whMTUc6J0V9ixVlpyCiwDvs= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855812; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=KQk1ajcAzxVFBv5LVexgdsWcNQxOZiGttVGP9q39TAQ=; b=hl9qU6FUwp9zG3UJD1JCsABdgkfGkVmANMp//teWl2ZB7YdFZ1Hjay3L20RtdsPjwOgVf6+KFH966WOnS7gSpBwljFpRguS29dltudLwIehmX/D05LggTG7qEZAAsyuYouFGcamfzuCuIkKbyTeax4oIowzmSGl8xhCI5UemUBE= 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=1670855812; 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:Message-Id:Reply-To; bh=KQk1ajcAzxVFBv5LVexgdsWcNQxOZiGttVGP9q39TAQ=; b=CzeIBxDSF5ptWTmcNzQ7onujnBGrHQPl9ohPzzhFagrWxMAGPxLMIL/cvNcGxE89 18VwEOEa2eTSCjs3AkbWT2fpKftsqgqpBxtmC/vTHofDZjX9JZYeX/8ZpD9zG7ahrjF a3djaJ9vkKch2RnpdaKCFM3qKXl5C6cvPwHEboXg= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855811088194.44364520679005; Mon, 12 Dec 2022 06:36:51 -0800 (PST) References: <7734e3c0299847c9a5c367e2bcf77a6a@mdc-berlin.de> <20221205152153.18545-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.11; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#59835] [PATCH 1/3] gnu: Add r-makecdfenv. Date: Mon, 12 Dec 2022 15:36:22 +0100 In-reply-to: <20221205152153.18545-1-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: <87cz8o3czj.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 59835-done Cc: 59835-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 (-) I applied this series with minor changes, thanks! -- Ricardo From unknown Thu Aug 14 21:51:25 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, 10 Jan 2023 12:24:08 +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