From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 18:26:32 2023 Received: (at submit) by debbugs.gnu.org; 24 Mar 2023 22:26:32 +0000 Received: from localhost ([127.0.0.1]:41600 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfprj-0004Jc-Ux for submit@debbugs.gnu.org; Fri, 24 Mar 2023 18:26:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:43336) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfpri-0004JV-Ad for submit@debbugs.gnu.org; Fri, 24 Mar 2023 18:26:31 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pfprh-0006L5-UB for guix-patches@gnu.org; Fri, 24 Mar 2023 18:26:30 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pfprf-00075w-VS for guix-patches@gnu.org; Fri, 24 Mar 2023 18:26:29 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:subject :subject:from:from:content-language:user-agent:mime-version:date :date:message-id:received; s=mdc; t=1679696763; x=1681511164; bh=mdQtC+V2kLVJ1o7YMUd1ekHqls/nSaLlYFJ7lmBby28=; b=BEdJ39VeHKT3 DqebUMLi8RUABExqncK7cBEoDgDicrLQNMVW94e57PtEkO1lNK64mL1DhrYJCpPe x8VW3YMx4G0GKQVsK2DnXXv2XJMjxnP2FnLydr4vflW2CI1yPXBGDOMLdTW5/rYx 4ZWVYa/aLprTsCnjegav5QzD3Nod/AU= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 6BA90300150 for ; Fri, 24 Mar 2023 23:26:01 +0100 (CET) Received: from [192.168.1.220] (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 15.1.2507.23; Fri, 24 Mar 2023 23:26:01 +0100 Message-ID: <4619c49d-2e96-49a5-7bf1-81877eb94696@mdc-berlin.de> Date: Fri, 24 Mar 2023 23:25:59 +0100 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:102.0) Gecko/20100101 Thunderbird/102.8.0 Content-Language: en-US, ro-RO To: From: =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= Subject: gnu: Add r-anota2seq, r-hybridmtest, r-apalyzer, r-org-sc-sgd-db, r-apcomplex, r-mdqc, , r-parody, r-arraymvout, r-arrayquality, r-beaddatapackr, r-beadarray, r-arrayqualitymetrics, r-repmis, r-setrng.. 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Sat, 25 Mar 2023 00:19:14 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: Date: Sat, 25 Mar 2023 00:18:50 +0100 Message-ID: <20230324231900.28367-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.662400-5.000000 X-TMASE-MatchedRID: OF2WlFkPn4APK2Dvdm/TZqoXHZz/dXlxKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvutvHF25zoU9GmC2qcPUEPtWM2x6EZ/S97Sc dpy2ZKwJOM4h+YsvDLlPSAWHDBcndrWL/xQJnm46rm7DrUlmNkIAy6p60ZV62HxPMjOKY7A9qHX ONfTwSQsRB0bsfrpPI34T9cYMsdwzdL8KCACz7cv24InidWbs6ALFXe9P1swdPIEig4S/HF8O72 /14i/nJD+oqALrPvIKqJudORveGBrMyP8xXiXl/DnZ8DMBydUXcUke23u350xU7OJY7bdPeD9iv /sJMsVc7Oyi/ulxQeKUgZdIaXg4f X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.662400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 6BD6E49D00AA5A0A63AE6D59439E23EB32000833652A060D9D2AE447FBB5CA4D2002:F X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 62428 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: -1.3 (-) Date: Fri, 24 Mar 2023 00:51:48 +0100 Subject: [PATCH 04/14] gnu: Add r-apalyzer. * gnu/packages/bioconductor.scm (r-apalyzer): New variable. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c58613bea3..3ae0dba919 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9354,6 +9354,51 @@ (define r-rcppnumerical @code{Rcpp}.") (license license:gpl2+))) +(define-public r-apalyzer + (package + (name "r-apalyzer") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "APAlyzer" version)) + (sha256 + (base32 "1iaz9ircfh5x3z5pibn5vnd4lbbr7m5ypk97xnizn22z41aqrxn3")))) + (properties `((upstream-name . "APAlyzer"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-deseq2 + r-dplyr + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggrepel + r-hybridmtest + r-repmis + r-rsamtools + r-rsubread + r-rtracklayer + r-summarizedexperiment + r-tidyr + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RJWANGbioinfo/APAlyzer/") + (synopsis "Toolkit for APA analysis using RNA-seq data") + (description + "The APAlyzer package performs @acronym{3'UTR, Three Prime Untranslated +Region} @acronym{APA, Alternative polyadenylation}, Intronic APA and gene +expression analysis using RNA-seq data.") + (license license:lgpl3))) + (define-public r-apeglm (package (name "r-apeglm") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:23 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:23 +0000 Received: from localhost ([127.0.0.1]:41649 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgs-0005kB-Oe for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:23 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:50233) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgq-0005jN-JQ for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:21 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1679699953; x=1681514354; bh=MeVX0Bk2E57msnI jWHtuPIhXbDV9yLTMYv2EeRFgdXM=; b=dGDh2OSPcLACrSpUwKQ8ExkSxLKTtid AhMPjIcE5wC2DrETo98GXigRRtFet6cbFD5aOR4QdeFeugcrCn60hwO4ryAySyUi R0VUoJO1SXFmx2FGRsog7bfxfgb6+QkSCdywtNkWKUFefdcs8XeZfuESg3CPDcJ4 6p6SZwbFoJd8= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id B1C9D30016F for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:13 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 01/14] gnu: Add r-anota2seq. Date: Sat, 25 Mar 2023 00:18:47 +0100 Message-ID: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--3.933000-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6ioK033WJkCkXjfR3d0weRm1/OiWPM9c7S+M w9GmoCTDtaS19CA2mWOa/i9HRzI0fYPVPAaE1AIJWeFNzK1vl0gK0ZgbTOeKUyiLz1Vtc/pWYDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07ba607moR85RGD4IDogaaVheJvX5hLxeooPQc Y4aTupiEFp+wBUhesaUw5xlhHUTSWyIjC0aI4hlUUzqxHl9/abO2k5GG6pBKvZpzWIFGCbEdAnz xkc/wOO+Yl/q6i1mnv1mO1iYLJDqT4cbBIKMuHq+68HqACCvKA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.933000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 33682B79A758EC4CEB62BF7610614F1883192248AB2F951E94D1D54EE7EE1BE92002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-anota2seq): New variable. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe446df67a..37b649a7d6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12069,6 +12069,42 @@ (define-public r-anota the data set is suitable for such analysis.") (license license:gpl3))) +(define-public r-anota2seq + (package + (name "r-anota2seq") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "anota2seq" version)) + (sha256 + (base32 "14ggggfa6mdqcb2hfvann9mb66s7a9nxlnh31zblb3mrrjizg1x3")))) + (properties `((upstream-name . "anota2seq"))) + (build-system r-build-system) + (propagated-inputs + (list r-deseq2 + r-edger + r-limma + r-multtest + r-qvalue + r-rcolorbrewer + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/anota2seq") + (synopsis "Transcriptome-wide analysis of translational efficiency") + (description + "The anota2seq package provides analysis of translational efficiency and +differential expression analysis for polysome-profiling and ribosome-profiling +studies (two or more sample classes) quantified by RNA sequencing or +DNA-microarray. Polysome-profiling and ribosome-profiling typically generate +data for two RNA sources, translated mRNA and total mRNA. Analysis of +differential expression is used to estimate changes within each RNA source. +Analysis of translational efficiency aims to identify changes in translation +efficiency leading to altered protein levels that are independent of total mRNA +levels or buffering, a mechanism regulating translational efficiency so that +protein levels remain constant despite fluctuating total mRNA levels.") + (license license:gpl3))) + (define-public r-sigpathway (package (name "r-sigpathway") base-commit: ef71e3290916583973724316e815cee840c1b6d8 -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:37 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:37 +0000 Received: from localhost ([127.0.0.1]:41660 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh7-0005lT-8M for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:37 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:53385) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgq-0005jL-JP for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:22 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699953; x=1681514354; bh=fT/IP6SUdlhubV7MYpVcfcjYz93/M00yNla37OGKLNU=; b=XeSagMK7mleN d1LNH0y9JOAEmw/5uHY63byzq9P260QqvPVDc941eicYqtRJQ+iNPo6Q8PYfkWV8 vzmu7oWxJ9g9s8BAnKTNL21Ggm2ugaht/YDN929CI8HkSmewGdl1dzVW5odyO6Jd fEQnYjD0Lch/UOfLnEvd7IgxRC1iTC4= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 07E14300124 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:12 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 03/14] gnu: Add r-hybridmtest. Date: Sat, 25 Mar 2023 00:18:49 +0100 Message-ID: <20230324231900.28367-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--8.986600-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIsD mFQEq0bLRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRqfMsy2bxlLv52/ 4Ak+0YK9gYGRmZe/Y+yEmqTfXa4IG25Xh6o1JmN87lKkz03w06+uLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWwCaCpZCqUcISz66hnNxSIiNGiaV/yFEEITVtlcPR/glWfxhTlCdaPQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.986600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 0B508CB8FEEAD6F11E0CD4157CEB03D8FB5138BCC90945482FFDF3DD58CCED912002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-hybridmtest): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 37b649a7d6..c58613bea3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -16248,6 +16248,36 @@ (define-public r-rsbml validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (license license:artistic2.0))) +(define-public r-hybridmtest + (package + (name "r-hybridmtest") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HybridMTest" version)) + (sha256 + (base32 "0mv092lq8548l306ghgvh8yka1fnyvs7w1yzfjzcchj8vlsb0qns")))) + (properties `((upstream-name . "HybridMTest"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-fdrtool + r-mass + r-survival)) + (home-page "https://bioconductor.org/packages/HybridMTest") + (synopsis "Hybrid multiple testing") + (description + "This package performs hybrid multiple testing that incorporates method +selection and assumption evaluations into the analysis using @acronym{EBP, +empirical Bayes probability} estimates obtained by Grenander density estimation. +For instance, for 3-group comparison analysis, Hybrid Multiple testing considers +EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test +of normality as weigth. Instead of just using EBPs from F-test only or using H- +test only, this methodology combines both types of EBPs through EBPs from Shapiro +Wilk test of normality. This methodology uses then the law of total EBPs.") + (license license:gpl2+))) + (define-public r-hypergraph (package (name "r-hypergraph") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:37 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:37 +0000 Received: from localhost ([127.0.0.1]:41662 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh7-0005lX-JM for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:37 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:57329) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgq-0005jQ-JT for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:22 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699954; x=1681514355; bh=nf70d9vCEAWj2gwaOpHDT+qRauHCZdNL0v1kdZRiuss=; b=A8q2tsMfky2v FMfPKFFygPAV929cjN5HBaKG8bqsP0UPWh+Ga+nX1tx6Io2RluaawXcrPK1HcNkp kVBvWNDW5J6BOr0dtH4d4GDvzF/GNHUQZYJbMRPeVPtSNYwgMg5dSbWTCx9PKDEv S/l0/RMokmb4ulvYmSyDeioCttwylNo= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8C36830018D for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:14 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 05/14] gnu: Add r-org-sc-sgd-db. Date: Sat, 25 Mar 2023 00:18:51 +0100 Message-ID: <20230324231900.28367-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--1.158400-5.000000 X-TMASE-MatchedRID: toN6SH028bX/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkELI5 /dPWFNfzRRa406V/YwyBUGewL2YXt8i5BCxh8k4DwLYk+NSxc5r4qCLIu0mtIPPlAor2K6GjmA0 yITMNzjl9LQinZ4QefCP/VFuTOXUTae6hIZpj4Mv3FLeZXNZS4CiM3WUt6LtFxZNFioJyRwIak6 XSr0vmNytcJiiFSX+h7LR8o9gyKs+36Q0ry+c9FZM8+496nWoci9fDe9jp4aCujf9ZG3IYiuGQ4 V+vGKrnWSgmpbFZnEI1kD2KtSTmq2Pbt5Stv2K5/Ox0TU9Ci5I= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.158400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: DC62EA9B71D0FA5384704EB5C0AC4B81EB5778F2C9F776152DFF95878E01FDF42002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-org-sc-sgd-db): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3ae0dba919..21aa3476c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -116,6 +116,27 @@ (define-public r-org-bt-eg-db based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) +(define-public r-org-sc-sgd-db + (package + (name "r-org-sc-sgd-db") + (version "3.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "org.Sc.sgd.db" version + 'annotation)) + (sha256 + (base32 "03b8m4p865kzhjj8zyhmc0ic0n4jyjdl4h8a8xny10b7xs6l0v9f")))) + (properties `((upstream-name . "org.Sc.sgd.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi)) + (home-page "https://bioconductor.org/packages/org.Sc.sgd.db") + (synopsis "Genome wide annotation for Yeast") + (description + "Genome wide annotation for Yeast, primarily based on mapping using ORF +identifiers from @acronym{SGD, Saccharomyces Genome Database}.") + (license license:artistic2.0))) + (define-public r-pd-mapping50k-xba240 (package (name "r-pd-mapping50k-xba240") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:38 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:38 +0000 Received: from localhost ([127.0.0.1]:41664 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh7-0005lh-Th for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:38 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:54915) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgr-0005jS-Px for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:23 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699955; x=1681514356; bh=CjbdIC2YgyjHhETMPd4Q/uY+u80g6JyEB0+EyFn4Omg=; b=GpgZofnEJUTk IWVmhal/d80lsZlPGUZnOhPIAmFZEY3u/IJflBtrirG+MbwluJzu13fpwITKntH/ 6Llo78kKWsTK3oBpthiQy6uPY3PyrlbTD/TP3YsU9L3UG6tcVbhj8kZ2Edmba308 5xfwNRv808pUQ0FFxNwmYCOs9YfD0yY= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id F41F2300195 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:14 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:11 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 02/14] gnu: Add r-repmis. Date: Sat, 25 Mar 2023 00:18:48 +0100 Message-ID: <20230324231900.28367-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10-0.932600-5.000000 X-TMASE-MatchedRID: n8dyCgqCzuv/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYnvkzitR82DjQYcH09cOokpqhcdnP91eXFxXefgn/TNQ8IubEPSkNnJ5t3 2Pj5vqMiNrUz3M8EKMuPRJuyjz/feJVNtzAuihDwG7bNEJKsuNheN9Hd3TB5GhJsTo2dS2dnW9n uzdghUMnAdP2YpewALYd00a6+9/yijxYyRBa/qJV/Hpl/zcOjl5MIx11wv+CPKayT/BQTiGrZ7H WIEiikzBZIh8P50cNSX3Q5VMTahXVsKjK9NtYcbNtVqZ3FwrtNvmoSVQVMCNAF/0QPCBPrEN4uK bQVHLmOFf9wsEfX1HgAQiNUjB8O8tOdWe/Uk/vuwZO9kmaWWvP8+E8vSQCkfySOb56URxsg= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.932600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 41A586DFA3E013FE9B3D1ED95B2A0C4D57338DD53D28C99F1B7E4BDD82A55E072002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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/cran.scm (r-repmis): New variable. --- gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a36c845479..325fec402b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2894,6 +2894,40 @@ (define-public r-selectr package is a port of the Python package @code{cssselect}.") (license license:bsd-3))) +(define-public r-repmis + (package + (name "r-repmis") + (version "0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "repmis" version)) + (sha256 + (base32 "0z5mjbsl24yjbl0aawr35grcal44rf2xbwv1hy7bdkms94ix79b5")))) + (properties `((upstream-name . "repmis"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-data-table + r-digest + r-httr + r-plyr + r-r-cache)) + (home-page "http://cran.r-project.org/package=repmis") + (synopsis "Miscellaneous tools for reproducible research") + (description + "This package is a colletion of tools to load R packages and automatically +generate BibTeX files citing them as well as load and cache plain-text and Excel +formatted data stored on GitHub, and from other sources.") + (license license:gpl3+))) + (define-public r-reprex (package (name "r-reprex") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:38 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:38 +0000 Received: from localhost ([127.0.0.1]:41666 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh8-0005lk-7D for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:38 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44857) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgw-0005jl-TM for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:27 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699956; x=1681514357; bh=VSG4+KkSq6jiD0FEsbOvnZPaqRBFudG4XyhRcYjkyvk=; b=Ni8S4KitIbQ8 YpvqCyc5/vWrPacyiZ9U/umuxBDmgKiaiAGTtAvXVpKIQMZjmIRAqdoqkq39d5zu jKMo8klahKNC2qBlAZIyzjvdXSTufXlQmjIY9WkSvOxNW4Nwk/40r9wBOcrPiV7M Tllev5tORkixE+WVjlxzYYP71PNwHM4= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id D795430019D for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:16 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 07/14] gnu: Add r-mdqc. Date: Sat, 25 Mar 2023 00:18:53 +0100 Message-ID: <20230324231900.28367-7-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--0.722000-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6rIGj0lq6L0YXjfR3d0weRny/Hx1AgJrrI1v /+HUjidRh0YasV59YfxJTjjs9yT6Yo8WMkQWv6iV3LAytsQR4e42j49Ftap9Eymsk/wUE4hqOvG 6VW4FmOZpK2j+/zzAuH6HKqegP5nmZpHaT7Nk8h6AJfBeyyoLclTs224IdfsnBbgAOnvaIzWEKn YY64E5ZgyQTsnD1LuIAEIjVIwfDvLTnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.722000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 9857609EAF0F6C011D707F19DD17F7CDD8795143DCC4564B051C7557ED3D1A192002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-mdqc): 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 71d65d64a5..39367dd927 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6968,6 +6968,31 @@ (define-public r-maser and visualizaton of alternative splicing events generated by rMATS.") (license license:expat))) +(define-public r-mdqc + (package + (name "r-mdqc") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mdqc" version)) + (sha256 + (base32 "1hn6m0z8q3jnzb0h8m29khgm0cx81cfs3s1j6hlg4wsrwkha1i3w")))) + (properties `((upstream-name . "mdqc"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-mass)) + (home-page "https://bioconductor.org/packages/mdqc") + (synopsis "Mahalanobis distance quality control for microarrays") + (description + "MDQC is a multivariate quality assessment method for microarrays based on +quality control (QC) reports. The Mahalanobis distance of an array's quality +attributes is used to measure the similarity of the quality of that array +against the quality of the other arrays. Then, arrays with unusually high +distances can be flagged as potentially low-quality.") + (license license:lgpl2.0+))) + (define-public r-metagenomeseq (package (name "r-metagenomeseq") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:39 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:39 +0000 Received: from localhost ([127.0.0.1]:41668 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh8-0005ls-Ka for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:38 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44263) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgw-0005jj-Su for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:27 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699956; x=1681514357; bh=XxHUkNOZ4eokr5w3C7Vdx8hfZOifJOEAJSD8zOYbdY4=; b=Kjwwgl6rJoSJ UBaTu+HOOxVt1thB1WA2GlD/ac4r+Ep1h0pjxV5YuMtUX8MASR/vNaDWyTLGYvnF qjN054n3QtqmLyRxum2dyvIfnayNRUlrbD/PQSJmo8M+Fb9UHbcob1Z+NMX6GAe1 bMSWOJtrI0jJ8LXdq1SvztXfNAvMCKs= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 6DF6A300199 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:16 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 06/14] gnu: Add r-apcomplex. Date: Sat, 25 Mar 2023 00:18:52 +0100 Message-ID: <20230324231900.28367-6-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.320200-5.000000 X-TMASE-MatchedRID: toN6SH028bX/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6r7wPook7ivAXjfR3d0weRiVIhha/jkqK4s8 u+Zeh+al9LQinZ4QefGWCfbzydb0gae6hIZpj4Mv3FLeZXNZS4CiM3WUt6LtFrGDsRPeZEf+z+L gjubLYqBp3yx0YBAue/PiFAYGEEmRLzJcrSYqXy0sOVnOKQgxW6kow3BV0MJ7KWOak9EyEngHT4 s6XK+DNWSgmpbFZnEI1kD2KtSTmq2Pbt5Stv2K5/Ox0TU9Ci5I= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.320200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 4C919D57CAD93EC0132E302B2BF625ECC1B70BD3A84178D48B98F3C3E494410F2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-apcomplex): 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 21aa3476c0..71d65d64a5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9420,6 +9420,31 @@ (define-public r-apalyzer expression analysis using RNA-seq data.") (license license:lgpl3))) +(define-public r-apcomplex + (package + (name "r-apcomplex") + (version "2.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "apComplex" version)) + (sha256 + (base32 "0ycchrdhx7zh62f0p0gxm7g58m2w3c2lfkaasrwydspd3jx0rsna")))) + (properties `((upstream-name . "apComplex"))) + (build-system r-build-system) + (propagated-inputs + (list r-graph + r-org-sc-sgd-db + r-rbgl + r-rgraphviz)) + (home-page "https://bioconductor.org/packages/apComplex") + (synopsis "Estimate protein complex membership using AP-MS protein data") + (description + "This package provides functions to estimate a bipartite graph of protein +complex membership using @acronym{AP-MS, affinity purification–mass spectrometry} +data.") + (license license:lgpl2.0+))) + (define-public r-apeglm (package (name "r-apeglm") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:39 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:39 +0000 Received: from localhost ([127.0.0.1]:41670 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh9-0005m1-0m for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:39 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:45073) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jp-1T for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699957; x=1681514358; bh=vllmIsZOEjk4QYNe9jsKDtc9mCmm2R8kT78Wa8FpiVg=; b=Zl2xG9U1y0E9 yK+NYhC3DRCUdw9z6DZ0M294uP0UjBW+V+iIo4IroOniAMC2ZzSi3g9l6f9wXPKD Ac7o7ao1gyAN6wwoBVb6up5OJdrnxo1jOI5ya5Tve7FJav/PffATT7QKmCOYpSeg C4/BnIaxlxX+hsJmtL+ZGxmiXrb63xA= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4A9503001A3 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:17 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 08/14] gnu: Add r-parody. Date: Sat, 25 Mar 2023 00:18:54 +0100 Message-ID: <20230324231900.28367-8-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--3.943400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZCWxD2S0xfx/OFG 8uiwVdY/F+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2KlfnlVv2XS+do85bE pzx6+0ruAFgmtvJJSFb83j9qM4FC18Tx4THFVLcE4sekoUOvVCECnJm2Z3T2S6sCZ0pbyKJJyxD 2EOkNO1b+P+STSeAJkoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.943400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 89469A79AD44A1C060B15D3027AAC540EDBC30629CF47D50C211061AFF5A3B7E2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-parody): New variable. --- gnu/packages/bioconductor.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 39367dd927..9f43c42bee 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -18999,6 +18999,27 @@ (define-public r-spp other functional sequencing data.") (license license:gpl2))) +(define-public r-parody + (package + (name "r-parody") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "parody" version)) + (sha256 + (base32 "12i5g4ai7a0p81kvqvz1qw099cy3g71n69pij8w760r3jn0c9ilw")))) + (properties `((upstream-name . "parody"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/parody") + (synopsis "Parametric and resistant outlier dytection") + (description + "The parody package provides routines for univariate and multivariate outlier +detection with a focus on parametric methods, but support for some methods based +on resistant statistics.") + (license license:artistic2.0))) + (define-public r-pathview (package (name "r-pathview") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:39 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:39 +0000 Received: from localhost ([127.0.0.1]:41672 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh9-0005m8-BC for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:39 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:34373) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jy-Fj for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699958; x=1681514359; bh=1yoUsl/j9D3TJ0c0M+ccciUJ9kkLnbpVfVxmE0jGE64=; b=Hf7VSEtSk+wc csBt2zNu7SvcIcENRpf5XtWVps5FxhBZW8BOoL592YIS5M4+alMBrP29oAntiISO 1psIIjqd1u22LpbqjSRIX301C0D1wrZNt2+hCkblltLb1y6po4muckAd9BfyobXt jfekTnoUWQZLleXsJNURFru9nCsVkZM= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id A8A6E3001BD for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:18 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:13 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 12/14] gnu: Add r-beaddatapackr. Date: Sat, 25 Mar 2023 00:18:58 +0100 Message-ID: <20230324231900.28367-12-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--1.554600-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPODnR iQbMAyihJNe/yL58XWfuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHY87 NwWBxSvhBPQd6lWNwpDnWWI8LLh4D28TY4LGPyU0apIb9znReA7qGBW9J0Yqj/c/LnF3l7WqYDT IhMw3OOX0tCKdnhB58I/9UW5M5dRNp7qEhmmPgy/cUt5lc1lLgKIzdZS3ou0UrnHTI07mmi3JGW UoimBufc5o+WNeCB1ubGxGgnOsaIpEy59Ba2lVvNGQKI8Iqn28nHNBsPal2ED8X7/6KqlDFDQ51 p2D4IpRZKCalsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.554600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: B0AC5ED89D21E244F08D1D2561DD108F65967CD92B4BF077FAD0F81939C5C47B2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-beaddatapackr): 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 7a904d3d08..e7ab9c983c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17963,6 +17963,26 @@ (define-public r-beadarraysnp performs copy number calculations and reports.") (license license:gpl2))) +(define-public r-beaddatapackr + (package + (name "r-beaddatapackr") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BeadDataPackR" version)) + (sha256 + (base32 "0309cvc9aq4nb06zysb7jvzd844pvw6jbjiqwhar6fg01cx255j0")))) + (properties `((upstream-name . "BeadDataPackR"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BeadDataPackR") + (synopsis "Compression of Illumina BeadArray data") + (description + "This package provides functionality for the compression and decompression +of raw bead-level data from the Illumina BeadArray platform.") + (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. -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:40 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:40 +0000 Received: from localhost ([127.0.0.1]:41674 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqh9-0005mG-Nq for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:40 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:49865) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jx-Eo for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699958; x=1681514359; bh=DWT3Cm/IROuXeaWMgtLwCbWTO96BayEuv2ZdTbIRG9k=; b=iUOyllIfAr8s 1d35KMOVlCgrlJ+UKf3/hL3XiyjAz8pTrJeez5vvX1qQ6BN/MVaDXF8JMiBXcWXu iLUF0OX2cekhGQ+keMI5UKdiLqmBcTVdEOsyqqBSIqkUWDOrG7Gz57tiKljHj5L3 2mWMLfWAT8uRDxxwyeTjS3xiWqZWrw8= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1202C3001B5 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:18 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 10/14] gnu: Add r-arrayquality. Date: Sat, 25 Mar 2023 00:18:56 +0100 Message-ID: <20230324231900.28367-10-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--4.783700-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeM3ZbGC9oP/O7Wc X/fVk9aGRRa406V/YwyBUGewL2YXt8Z8zsjIitoJ71Wx2uUbPLclSmDuA9gjEVVMJlS9HCuzGg6 YSQd92h57MSP7SLpuGM+e/4CnFGik8f+64gLLEwLdCok3ibXlQeuLFZZYlisfHxPMjOKY7A9wK7 mZ44aKbi8z+bJ2nm9UKrauXd3MZDUal568aygjl6tO5InZNwbJJOSKosHSuiqJkErMcswT/X3GH u67ZOgPaUlfxqclV0qZ7Z76m2H8uz0zXC8ftXDbDxJaJjSdPyku41Tl3hgJxQ1BJAU2fLzi8Zck wl0EeMYqAOTwOHULsbmKSUdpIXl3ftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.783700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 22FF38CABA2830017324679FBF21F06C832E8F5EC7ED9518AA978C9084ECBA8A2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-arrayquality): 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 62cd786842..7a904d3d08 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3251,6 +3251,31 @@ (define-public r-arraymvout error rate.") (license license:artistic2.0))) +(define-public r-arrayquality + (package + (name "r-arrayquality") + (version "1.76.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayQuality" version)) + (sha256 + (base32 "0b5q71bpl9ln26622jvchd4f9i4kwayqkm9b75yj0a69imbfcn4s")))) + (properties `((upstream-name . "arrayQuality"))) + (build-system r-build-system) + (propagated-inputs + (list r-gridbase + r-hexbin + r-limma + r-marray + r-rcolorbrewer)) + (home-page "http://arrays.ucsf.edu/") + (synopsis "Assessing array quality on spotted arrays") + (description + "This package provides functions for performing print-run and array level +quality assessment.") + (license license:lgpl2.0+))) + (define-public r-asafe (package (name "r-asafe") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:40 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:40 +0000 Received: from localhost ([127.0.0.1]:41676 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhA-0005mN-1u for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:40 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:43281) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005jq-2Z for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:28 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699957; x=1681514358; bh=6QcW3L17Rq4Y/u9pytApGq78a8H0WcCnye/qLVMz2TU=; b=myrlqTPnBtIh TFQ92KyGAnjtoxncFzwIlxQg/AcQ199sT8XvYHJhLIdl+sEY0mqJXHWzsS2/2Yta uV/xnvC9m8CA+zZBR1wxJqOj0QM2Lh1sijx02L3CG6NNt5HqbC35pjBIJNwC1u78 Ymq9H2kYCpvRrpWYG+YMnRQvBnaen94= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id A8F4B3001AD for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:17 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 09/14] gnu: Add r-arraymvout. Date: Sat, 25 Mar 2023 00:18:55 +0100 Message-ID: <20230324231900.28367-9-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--0.774700-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYnvkzitR82DjQYcH09cOokpqhcdnP91eXFxXefgn/TNQ8IubEPSkNnJR3V 9V6dMWSWKbindmE5bmEwECQaT0DBZIrDBDJBPVs6uG6vp8tkx53iZgkcDEaRzk5Oq0M3nL1DEvo wQGF7Hg4jQSOd69r3fmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5dahHHRNtA1e4Hhm lAwuGnTE41Ztc+fFvlZl6qaUBLo2cbJFAtk5vWZY17A/rrTegklfnzEqph9AAnEDrBhOrVryndM Ht5d/doNQSQFNny84vGXJMJdBHjGKgDk8Dh1C7G5iklHaSF5d37cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.774700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 5C5409C88FEAE7475460F4219536FB1D5CA4863C88AD81CCC40751FD0D8036F42002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-arraymvout): New variable. --- gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9f43c42bee..62cd786842 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3215,6 +3215,42 @@ (define-public r-arrayexpress structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (license license:artistic2.0))) +(define-public r-arraymvout + (package + (name "r-arraymvout") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayMvout" version)) + (sha256 + (base32 "0g66s64n4qlvhkanp33bbvpi93rsdx5xq0mjr96d0195qbf6k156")))) + (properties `((upstream-name . "arrayMvout"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-affy + r-affycontam + r-biobase + r-lumi + r-mdqc + r-parody)) + (home-page "https://bioconductor.org/packages/arrayMvout") + (synopsis "Multivariate outlier detection for expression array QA") + (description + "This package supports the application of diverse quality metrics to AffyBatch +instances, summarizing these metrics via PCA, and then performing parametric +outlier detection on the PCs to identify aberrant arrays with a fixed Type I +error rate.") + (license license:artistic2.0))) + (define-public r-asafe (package (name "r-asafe") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:40 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:40 +0000 Received: from localhost ([127.0.0.1]:41678 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhA-0005mU-Dd for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:40 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:55909) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005k4-Rc for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:29 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699959; x=1681514360; bh=uwmw+G5iWXE4KdKFMj79uywLHjdincbMT4gg1qislE8=; b=G9LEepANSeCR Ypr4tW6grGWnd/6T87oW7tMR0lm9E2dyNxmgZfX9NTaI3ci+QdRYxZqGxbqmTplq emP9yxjyx7FGBS4DKUaViNkxTu840qv8BHxrQcj2JlYHEV8qPaz6MsmpN8de1Epg uMCScmvD2DIAFklxs02aXxBXn7jnq7U= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1FAD13001C1 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:19 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:13 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 13/14] gnu: Add r-beadarray. Date: Sat, 25 Mar 2023 00:18:59 +0100 Message-ID: <20230324231900.28367-13-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.238000-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6rIGj0lq6L0ahHrZE2+S866Y5ZGw7wyeHEpM Y0o/BrKdyQB4UAGIVrzgELkIsyIqM0N7DjAdxZNTi8zVgXoAltsIJ+4gwXrEtwrbXMGDYqV+i5u /VvsFaHR8XkxC85xWeJY6AKHAFL88yiOD9xnnZjT5/EAmAmUoaXxkIOPs/mxH9WYIiq13f/x88F JLWCwbOvNj0INejLTzinpP+yXTbVShCDgyssE8uo3yYJV8x0OrMUVc0s17dsX/q4TD2v7K1 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.238000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: D5FBD11E844786B796B39C8CEC7464734CA73E13D4FF979A987272DDC2AE17742002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-beadarray): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e7ab9c983c..6c114efd21 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -17943,6 +17943,40 @@ (define-public r-beachmat matrices.") (license license:gpl3))) +(define-public r-beadarray + (package + (name "r-beadarray") + (version "2.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beadarray" version)) + (sha256 + (base32 "0fr24gj6h2rr1r4l3n8myjaihjqi5yinwdsxqa5ih8m3v72dlrby")))) + (properties `((upstream-name . "beadarray"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-beaddatapackr + r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-hexbin + r-illuminaio + r-iranges + r-limma + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/beadarray") + (synopsis + "Quality assessment and low-level analysis for Illumina BeadArray data") + (description + "The package is able to read bead-level data (raw TIFFs and text files) +output by BeadScan as well as bead-summary data from BeadStudio. Methods for +quality assessment and low-level analysis are provided.") + (license license:expat))) + (define-public r-beadarraysnp (package (name "r-beadarraysnp") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:41 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:41 +0000 Received: from localhost ([127.0.0.1]:41680 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhA-0005mc-Pf for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:41 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44897) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgz-0005kP-2q for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:29 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699960; x=1681514361; bh=hw63NtPPgj/cEoqZIlmcR95LDRQlFpJgL8NaL5NGHRE=; b=CsFiaK4V6J5B 1oTgNuCJQgf8PPyAfUdqANnluk2lubvHkjbEOFbU7qHP0TwbmUmdxtVSw6XhBNvZ RoezklMDT7YS/O00y0oM9fgTK+kNzI3+rCpiurinfw5os1gob1Jcz8Uv+LGBMdNJ HgnTka/quiQeQ3kQ2+IEcytYrXpSTPg= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 1F0CC3001CD for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:20 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:13 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 14/14] gnu: Add r-arrayqualitymetrics. Date: Sat, 25 Mar 2023 00:19:00 +0100 Message-ID: <20230324231900.28367-14-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.105400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6rIGj0lq6L0YXjfR3d0weRhh1mpCXNVC8qbd h+ZHR69rF+KCpGE37CJsoi2XrUn/J8m+hzBStansfRoCwBzgRYsK21zBg2KlfCQvlWYtoEBHLqa IYEBIRhIU3Gs62OX1uQndELcZsq4lJ7Z0rexjc6sOFCT51VwnScK6BPLcMIqcshzQkxO+/gdD1q km1QqYayBr8AT+uPPcoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.105400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 08CC6DD37CC7598EFEF6A3ECF6F2323DB216039CE3511D85806A3ED7182D40602002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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-arrayqualitymetrics): New variable. --- gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6c114efd21..8792c94d29 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3190,6 +3190,44 @@ (define-public r-antiprofiles tumor samples from healthy controls.") (license license:artistic2.0))) +(define-public r-arrayqualitymetrics + (package + (name "r-arrayqualitymetrics") + (version "3.54.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayQualityMetrics" version)) + (sha256 + (base32 "0jz9b3f8x1aal4sskq1a09jpavhm8alggwbj3ka42fb89xymrz33")))) + (properties `((upstream-name . "arrayQualityMetrics"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-affyplm + r-beadarray + r-biobase + r-genefilter + r-gridsvg + r-hmisc + r-hwriter + r-lattice + r-latticeextra + r-limma + r-rcolorbrewer + r-setrng + r-svglite + r-vsn + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/arrayQualityMetrics") + (synopsis "Quality metrics report for microarray data sets") + (description + "This package generates microarray quality metrics reports for data in +Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). +One and two color array platforms are supported.") + (license license:lgpl2.0+))) + (define-public r-arrayexpress (package (name "r-arrayexpress") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 24 19:19:41 2023 Received: (at 62428) by debbugs.gnu.org; 24 Mar 2023 23:19:41 +0000 Received: from localhost ([127.0.0.1]:41682 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqhB-0005mk-5n for submit@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:41 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:53231) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pfqgx-0005k5-S3 for 62428@debbugs.gnu.org; Fri, 24 Mar 2023 19:19:29 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1679699959; x=1681514360; bh=bVqr6m5qcZ+cXnDU8yXpAzhBqNT3EtmHdB1s/jIDx+E=; b=D1Gvj3rhdABW FRcFqOqMCmpb5EbAgBJk0QvOAzcq3zzrBFm5XFCJuXhXvGP6eWQJP8/DiSxH0pMv gSAhwBFl5f+xwInzIE3s02QP0hceLqmPYQzefkYPNntoMdR3hG72j+oVyPEzZL+r U3iQ1rX51Ja4jtZFU/VHmodRWwKl8yc= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8C7CE3001C5 for <62428@debbugs.gnu.org>; Sat, 25 Mar 2023 00:19:19 +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 15.1.2507.23; Sat, 25 Mar 2023 00:19:12 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <62428@debbugs.gnu.org.> Subject: [PATCH 11/14] gnu: Add r-setrng. Date: Sat, 25 Mar 2023 00:18:57 +0100 Message-ID: <20230324231900.28367-11-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.2 In-Reply-To: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> References: <20230324231900.28367-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-AS-Result: No-10--2.544200-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90Badv+F8ucSI031Nfxfj2zOp/958oU3WcKY5ZGw7wyeHiwO YVASrRss7RZ9SX+rqZS1h1eUc+p680N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jFnjKVTYbDMDEQd G7H66TyN+E/XGDLHcMWpoRm6v3svZWb0mb4EdHMQ3BXaA1V5BHBcpNiZN6sQLm0Ju/KvlWS9XVd ckExYCRAKR1s4zi9sJpV+rqK0DCKOBiOleQmdrd3FJHtt7t+dMVOziWO23T3g/Yr/7CTLFXOzso v7pcUHilIGXSGl4OHw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.544200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27524.003 X-TM-SNTS-SMTP: 7C79A6904B47EB2567C2FA24EAC0495D33F3A6C442B25B955939C0E2BA9C27252002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 62428 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/cran.scm (r-setrng): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 325fec402b..bfcafea355 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -20170,6 +20170,28 @@ (define-public r-bedr additional utilities for genomic regions processing.") (license license:gpl2))) +(define-public r-setrng + (package + (name "r-setrng") + (version "2022.4-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "setRNG" version)) + (sha256 + (base32 "09089vr5x8snwxh38kdhgpjl3jl7zrk056f6f9a2jg5lsrmnxh31")))) + (properties `((upstream-name . "setRNG"))) + (build-system r-build-system) + (home-page "http://distr.r-forge.r-project.org/") + (synopsis "Set (normal) random number generator and seed") + (description + "This package provides utilities to help set and record the setting of the +seed and the uniform and normal generators used when a random experiment is run. +The utilities can be used in other functions that do random experiments to simplify +recording and/or setting all the necessary information for reproducibility. See +the vignette and reference manual for examples.") + (license license:gpl2))) + (define-public r-sets (package (name "r-sets") -- 2.39.2 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 30 19:00:16 2023 Received: (at control) by debbugs.gnu.org; 30 Mar 2023 23:00:16 +0000 Received: from localhost ([127.0.0.1]:59814 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pi1Fg-0005Sr-1G for submit@debbugs.gnu.org; Thu, 30 Mar 2023 19:00:16 -0400 Received: from smtpm1.myservices.hosting ([185.26.105.232]:37158) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pi1Ff-0005Sk-1j for control@debbugs.gnu.org; Thu, 30 Mar 2023 19:00:15 -0400 Received: from mail1.netim.hosting (unknown [185.26.106.173]) by smtpm1.myservices.hosting (Postfix) with ESMTP id 1B898207FC for ; Fri, 31 Mar 2023 01:00:13 +0200 (CEST) Received: from localhost (localhost [127.0.0.1]) by mail1.netim.hosting (Postfix) with ESMTP id A3D0B8009A for ; Fri, 31 Mar 2023 01:00:10 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at mail1.netim.hosting Received: from mail1.netim.hosting ([127.0.0.1]) by localhost (mail1-2.netim.hosting [127.0.0.1]) (amavisd-new, port 10026) with ESMTP id quAab374MQkf for ; Fri, 31 Mar 2023 01:00:10 +0200 (CEST) Received: from [192.168.1.239] (unknown [10.192.1.83]) (Authenticated sender: lumen@makinata.eu) by mail1.netim.hosting (Postfix) with ESMTPSA id 53A0380098 for ; Fri, 31 Mar 2023 01:00:10 +0200 (CEST) Message-ID: <74912071-f536-c8bc-4711-db295b4da0e6@makinata.eu> Date: Fri, 31 Mar 2023 00:00:01 +0100 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:102.0) Gecko/20100101 Thunderbird/102.9.0 Content-Language: en-US To: control From: Bruno Victal Subject: control-msg Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: control 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 (-) # done with 5c131aff691fa1cb0fafe71b5f2795902ae056a7 close 55819 # control fail? close 45449 # no longer relevant close 33078 # tags tags 62551 patch tags 62503 patch tags 62461 patch tags 62443 patch tags 62428 patch tags 61226 patch tags 59893 patch tags 59852 patch tags 49451 patch tags 49207 patch tags 44258 patch quit From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 04 05:07:54 2023 Received: (at 62428-done) by debbugs.gnu.org; 4 Oct 2023 09:07:54 +0000 Received: from localhost ([127.0.0.1]:41535 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qnxrG-0001qU-1w for submit@debbugs.gnu.org; Wed, 04 Oct 2023 05:07:54 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21711) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qnxr7-0001qE-6B for 62428-done@debbugs.gnu.org; Wed, 04 Oct 2023 05:07:51 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1696410443; cv=none; d=zohomail.com; s=zohoarc; b=PmOW7bp1CDA1JKz32fYyF635J8TjEvMCQHVza0Neebgx8qgTBRLv74cn9cQSVOtbMiqXbtbXnk4LzTsvkriCHjWAHCXJr2LYrNpzKDjzyfGTzLbFUYo3u3mH2T9dSrU7mvcmcSdsctmAAv+sMCxueWFTTqKDwRlC5WpwX3oCoEw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1696410443; h=Content-Type:Content-Transfer-Encoding:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=EE1DuPOYHOOgI531Agj8u019l8Q+l65o6cUKRfZyVTI=; b=KZNXshbxxM1EXcID1l7oAKbWCSSCb0F049vwJh2Q330uOIgK5DRQM4NSOqz0jRZWP8PRekn+AFE4NjcgumhbNsqgFppVlUp7k0kYmGo2SPAlz1HstsKJxd50xLV36+t9wNNo7PtrYHq8ZlzQKAyYzHaIyw2pyDn1lGBaC410PBc= 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=1696410443; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To:Cc; bh=EE1DuPOYHOOgI531Agj8u019l8Q+l65o6cUKRfZyVTI=; b=gcMkCZ05haaQCTAwAn96LFY04B+/DDFgPpud7VKhlWAO5Cut/67sW9NUoHqi5Rzj MuFLN2oY3GaP98GgHpZgxFASsmkOWabiYN2Tl9+kbhKwvgWpUtaGh2NUPXK6cBigOPb ZxnlHkoVCBrkxYCkrYmf9GYTEsR438KRjhaD4e4U= Received: from localhost (i5E862C8A.versanet.de [94.134.44.138]) by mx.zohomail.com with SMTPS id 1696410441409247.75251076339134; Wed, 4 Oct 2023 02:07:21 -0700 (PDT) User-agent: mu4e 1.10.7; emacs 29.1 From: Ricardo Wurmus To: 62428-done@debbugs.gnu.org Subject: gnu: Add r-anota2seq =?utf-8?Q?=E2=80=A6?= Date: Wed, 04 Oct 2023 11:06:07 +0200 Message-ID: <878r8irc1l.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: 62428-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 (-) I=E2=80=99ve rebased this, updated all packages, fixed indentation, replaced gexp syntax with simple quote, and removed duplicates. Thanks for the patches! Closing. --=20 Ricardo From unknown Sun Jun 22 07:36:13 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 01 Nov 2023 11:24:09 +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