From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 08 10:58:48 2022 Received: (at submit) by debbugs.gnu.org; 8 Apr 2022 14:58:48 +0000 Received: from localhost ([127.0.0.1]:35544 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq4W-0006Rj-A8 for submit@debbugs.gnu.org; Fri, 08 Apr 2022 10:58:48 -0400 Received: from lists.gnu.org ([209.51.188.17]:33636) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq4T-0006Rb-WC for submit@debbugs.gnu.org; Fri, 08 Apr 2022 10:58:46 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52690) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ncq4T-00064a-Mr for guix-patches@gnu.org; Fri, 08 Apr 2022 10:58:45 -0400 Received: from mail-wr1-x42f.google.com ([2a00:1450:4864:20::42f]:39785) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ncq4S-0000wY-9d for guix-patches@gnu.org; Fri, 08 Apr 2022 10:58:45 -0400 Received: by mail-wr1-x42f.google.com with SMTP id q19so13255081wrc.6 for ; Fri, 08 Apr 2022 07:58:43 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=hZ7S7urLDLTzNIgfixK+CHOFLl0QShooO53tlZeGRAY=; b=ePczom5OWzmEJOToeIg06S8UdUx3tCQC8LHyvGRn1Ophn2PApF2620MVJPAGjbE/ru vQUZUc+F9iw1M06XaqJy9EiDXya8gyS6wOUWJWFjodu373g0NnGrbEkRUe2zezotCSDy lw49NYl+CshGasrHJyG0G/iyg0tRvJtpDIVBRcrMitIxUHY2KeSM5nCsejiLFrhVQw/Z +3AyOqeSLWX+EZkxMHlLVumjGreF2ZxoonAjSgUXuji0LDLtMl0yqdVdTEmyPilxwUSG qBqLyvq5Q4mR6qcbGLvZgb5bgLe5vA6JrjBhhx8VRKGhNGpaUGAGCftyr4fB8qZi6s70 vt9w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=hZ7S7urLDLTzNIgfixK+CHOFLl0QShooO53tlZeGRAY=; b=m+RMLrzTkgn2ikl21aEmbJUU5hT2fLWCRmA0WO1N5bGtJJ0RFAw26yDe8Hqh38OtXe JVf8VuE/BVb++cMI/PZbPqwx88lI9iJfYdWk+CO+r/CiR080q5NarTZHeV+kmkTJbTDq 5R6JT+gfSdO16BuSGQKocfk+fpeG++GL1JqrFUbV/raB5tynlPEPvkHwT+0UfXILdTO3 UagXGbv1HWCh2ZJxrx8tt7F120ff1Lf4fs+9suQsnMjzoR/U8wXFFUqTMFzelMwa1NcH 5gtYeRYLkswgqNDSjwrv8taO7uJDx08Ugw5MWHeHHkRa4ri/69XBrLTD1MxewmV3UmQG aYMg== X-Gm-Message-State: AOAM533QTeUZO4FLrHvZn65bf9Pnrcw0Rolu0CiZcVOI2GKW68aNsr+L /iexgrAJa7xuNZ1jUG/d51Y6xlp6HmA= X-Google-Smtp-Source: ABdhPJz7jKfQz8Z+PQWhXJY1GX18hnbvc94OGeT55qaFB0AOX9aijGAFllo4gycVr/2fhUcap+jstA== X-Received: by 2002:a5d:64eb:0:b0:205:d418:4798 with SMTP id g11-20020a5d64eb000000b00205d4184798mr15324476wri.11.1649429922009; Fri, 08 Apr 2022 07:58:42 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s17-20020adfdb11000000b001f02d5fea43sm20123381wri.98.2022.04.08.07.58.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 07:58:41 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 0/3] Add r-copykat and dependencies Date: Fri, 8 Apr 2022 16:58:29 +0200 Message-Id: <20220408145829.3344728-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 X-Debbugs-CC: rekado@elephly.net Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::42f; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x42f.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: zimoun 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: -2.3 (--) Hi, I hope that all is fine. Cheers, simon zimoun (3): gnu: Add r-paralleldist. gnu: Add r-dlm. gnu: Add r-copykat. gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++ gnu/packages/cran.scm | 53 +++++++++++++++++++++++++++++++++ 2 files changed, 91 insertions(+) base-commit: 09ec1d65613e111a3ee2cbeda350441e058deb8f -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 08 11:00:12 2022 Received: (at 54790) by debbugs.gnu.org; 8 Apr 2022 15:00:12 +0000 Received: from localhost ([127.0.0.1]:35553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5r-0006W9-LN for submit@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:11 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:42922) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5p-0006Ug-Hw for 54790@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:10 -0400 Received: by mail-wr1-f51.google.com with SMTP id r13so13257688wrr.9 for <54790@debbugs.gnu.org>; Fri, 08 Apr 2022 08:00:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=yzSxJllHckq113wn6zoibfSTGdkE/qY7tXbbvW9Qsnw=; b=mXr9lyUTjsHrVjxNEa1R+7M9tNBNSy+RM6/jp1f3x8o9filazchHzkePupTyHpPu0W Atz4WUYL1epCgL6IohjwvO0vHob4n73oZAE8pkctZfD34Ss/oUNDsPHVTlfoLzy9i0R4 YqekfeCs5xm+aAc7Ex9F4KjcW8/4esFfCjqSkBjp3ptQOgMr1JTvWIM9/fAhJTv3ovpz +TI9WSauZN6U/wS3nALGT3g5a4DRFoZ5MPA91cwzYPdVFt6rg+Wfk4r7rZLodAuEY8bm fNX8jARx8UcoZM34MESnPQyn43TgURwP+IIPuSPcofcsHW3DsoMvwmJMKXvF5NxcD2/m OzTg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=yzSxJllHckq113wn6zoibfSTGdkE/qY7tXbbvW9Qsnw=; b=DY8U5QZJca7S+Rg5aCB9GaBkAtwLSbnmobE0LX/XUqv4s68IWRWYMeph39x80/5aZs bo8SArE42ZuuxwiiNYRu4t0MAYy8LYxfy4/UzQx1DLDu7FkqHQH6tvcy44ndHB8CuIN8 WI7o+WnSChSO6bPNxqjG3ai8slfxC50y8YJe5PKWbYGwONsHgxSFXMpQDRXUbN9yR3TJ a8opoWTk7rTPjfuTlww7p/vWTDW1JEJMicc1yS7Hk1RvYVhZZE5P86ZkgeDI4KZVMKVZ dYWQIQ5JZ15AzMQKaw5BOqJMKvIzTTXWN+xiXTQFVhiHxo3g7fPIcx1rx3rDfynLvS4d qNvQ== X-Gm-Message-State: AOAM533oVZnnwJK1NOqFlpm0DrG1k55G6QqzN77LLai8n/osF6CMpvFN onPkd0aCDpEoKQU6wV3RghKHQPpk/x8= X-Google-Smtp-Source: ABdhPJxfLkEXx61f5VHCQXbPtHzpveQ2o0oc8ENxjWi637MqTjtCZe8sCZ31bZnkkXNEK22+CzDDBg== X-Received: by 2002:a05:6000:1f9a:b0:207:9ad9:e300 with SMTP id bw26-20020a0560001f9a00b002079ad9e300mr1410346wrb.562.1649430003494; Fri, 08 Apr 2022 08:00:03 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t185-20020a1c46c2000000b0038e7092025bsm10388554wma.20.2022.04.08.08.00.01 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 08:00:02 -0700 (PDT) From: zimoun To: 54790@debbugs.gnu.org Subject: [PATCH 1/3] gnu: Add r-paralleldist. Date: Fri, 8 Apr 2022 16:59:52 +0200 Message-Id: <20220408145954.3345224-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54790 Cc: zimoun 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 (-) * gnu/packages/cran.scm (r-paralleldist): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index be77a57f28..b9ea1144f2 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1074,6 +1074,39 @@ (define-public r-pacman functions which can speed up workflow.") (license license:gpl2))) +(define-public r-paralleldist + (package + (name "r-paralleldist") + (version "0.2.6") + (source + (origin + (method url-fetch) + (uri (cran-uri "parallelDist" version)) + (sha256 + (base32 "01ly4hxwa64a0ya5gla8rvv72s9mcknsfznivjkh937pbjwb7iih")))) + (properties `((upstream-name . "parallelDist"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo r-rcppparallel)) + (home-page "https://github.com/alexeckert/parallelDist") + (synopsis "Parallel Distance Matrix Computation using Multiple Threads") + (description + "This package provides a fast parallelized alternative to R's native +'dist' function to calculate distance matrices for continuous, binary, and +multi-dimensional input matrices, which supports a broad variety of 41 +predefined distance functions from the 'stats', 'proxy' and 'dtw' R packages, +as well as user- defined functions written in C++. For ease of use, the +'parDist' function extends the signature of the 'dist' function and uses the +same parameter naming conventions as distance methods of existing R packages. +The package is mainly implemented in C++ and leverages the 'RcppParallel' +package to parallelize the distance computations with the help of the +'TinyThread' library. Furthermore, the 'Armadillo' linear algebra library is +used for optimized matrix operations during distance calculations. The +curiously recurring template pattern (CRTP) technique is applied to avoid +virtual functions, which improves the Dynamic Time Warping calculations while +the implementation stays flexible enough to support different DTW step +patterns and normalization methods.") + (license license:gpl2+))) + (define-public r-pheatmap (package (name "r-pheatmap") -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 08 11:00:12 2022 Received: (at 54790) by debbugs.gnu.org; 8 Apr 2022 15:00:12 +0000 Received: from localhost ([127.0.0.1]:35555 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5r-0006WC-V7 for submit@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:12 -0400 Received: from mail-wr1-f41.google.com ([209.85.221.41]:44908) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5q-0006Uh-2D for 54790@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:10 -0400 Received: by mail-wr1-f41.google.com with SMTP id b19so13248636wrh.11 for <54790@debbugs.gnu.org>; Fri, 08 Apr 2022 08:00:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=QezaVBJFJaEsjN0toj/LUr+drqv+xCkYVufm827opvk=; b=RvvlglJtyUngTErur3ESvRJbpWGITfLooFI2i5CiZ3Hd3oHMuVULjY03Wghjb4dlKl xxcBrx4xsJtAMriBZnTTj0Q7JEf5P+tUumjDS+f1cGFH01uFU8KhLWg+Vz1pZZmLzcAm y/oixUn1vD86OY3OTqyySLLzAi6+IV95+36AAakGY8qq0FWavXIuL7oPQQvzQNJdm3g6 MioeNsFzsvTGL3KUGJcN8dXmBcAmW1j4itfs7x8cBTJVZJd49HKkhVVS0PmyECJatFTG 5zu9xlIhm5TIPQS0rGOks/0kTysVGS4NGFYOCwpbSRlu7kQb4TmZjsc0xZ61T5dsVcj/ GBUQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=QezaVBJFJaEsjN0toj/LUr+drqv+xCkYVufm827opvk=; b=4O/fWm6iFFGwoqRRSy/Uw4NyPX2+XD98492gDLfOwKxv9tHLrzVKYX4HAGeEJjL6wS LxcmM9Ig/ia4a00pmj2CZJBE1U8mMCZM63aniSpVZSpt0hnBSa8PqfDRQfU44Nzjwo8b HRUyhrBr7eqj0LGRULL4rihCnZnd8sQWyvJ4ezjkObOzEnTiyaQv4++HMCCi9vXiQ+7+ 7g3SVdTF8QEXBrBQae4q/VK/daae+l4hjo63zeSA6XNbBj7GuxHPrYzn065c0QZLwHrl OM5maaBU33vVHf6sIVJzjqcXaPO8UL4Nuiqi+kHDisYW5D+xrIS932CVhYI1QwSSwHnh /Ejg== X-Gm-Message-State: AOAM533kToA9QvnCg7fWlmnr/01aSTIt/OK4MqeTTtwHmg4/JxFjuzpg ZxtaYsaP2V3QWEUVNr42lANZTxnttK8= X-Google-Smtp-Source: ABdhPJyagBXrGPpU7eJmBUKBUwQYiXQsCUEbDiSAKIbmHqecLn7KPqrS0ApQUyyw7vao2TNnF7Q+dg== X-Received: by 2002:a5d:6205:0:b0:1e4:b3fd:9ba8 with SMTP id y5-20020a5d6205000000b001e4b3fd9ba8mr14924471wru.426.1649430004161; Fri, 08 Apr 2022 08:00:04 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t185-20020a1c46c2000000b0038e7092025bsm10388554wma.20.2022.04.08.08.00.03 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 08:00:03 -0700 (PDT) From: zimoun To: 54790@debbugs.gnu.org Subject: [PATCH 2/3] gnu: Add r-dlm. Date: Fri, 8 Apr 2022 16:59:53 +0200 Message-Id: <20220408145954.3345224-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220408145954.3345224-1-zimon.toutoune@gmail.com> References: <20220408145954.3345224-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54790 Cc: zimoun 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 (-) * gnu/packages/cran.scm (r-dlm): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b9ea1144f2..5a852af4b7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -659,6 +659,26 @@ (define-public r-clipr the system clipboards.") (license license:gpl3))) +(define-public r-dlm + (package + (name "r-dlm") + (version "1.1-5") + (source + (origin + (method url-fetch) + (uri (cran-uri "dlm" version)) + (sha256 + (base32 "1aksm66sfa7ipl5xgs4j5giac7q2m744wjl40mva56xn6i674h4r")))) + (properties `((upstream-name . "dlm"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=dlm") + (synopsis "Bayesian and Likelihood Analysis of Dynamic Linear Models") + (description + "This package provides routines for Maximum likelihood, Kalman filtering +and smoothing, and Bayesian analysis of Normal linear State Space models, also +known as Dynamic Linear Models.") + (license license:gpl2+))) + (define-public r-zoo (package (name "r-zoo") -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 08 11:00:12 2022 Received: (at 54790) by debbugs.gnu.org; 8 Apr 2022 15:00:13 +0000 Received: from localhost ([127.0.0.1]:35557 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5s-0006WL-DM for submit@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:12 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:44910) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5q-0006Uj-BP for 54790@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:10 -0400 Received: by mail-wr1-f42.google.com with SMTP id b19so13248659wrh.11 for <54790@debbugs.gnu.org>; Fri, 08 Apr 2022 08:00:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=RSVPYpp1ByIX+MOdPLR+WqEBg5BdEHD2ys5Dwm3oOIA=; b=j+hXwvUXMbaWqOMo9lk/3RpKHTxFGBAK6Qgf5aVGuG55YXHtYcj1rPPJnxw3G2CTc9 kzmhaP82A9kUDpt+ycR5K3gIGoaZ4S5bMExQ0TyWHdGnY3uFEngdf3Pe5l0gptz04rs9 is7c/29hD3nduBHVCfwuJX2kIO/aBKgnKyGrUoLUQLVdR8c9T3+aIsJzUdrXDJMxLZL5 UqMuzXTHO8MIKySkL7vR2Vep9EjRNWQtnj+agcQu6B9EXUzqm3MiHSSS3YUzr8XYXZn5 NVYBt/h1BQTJGsVzqbT7cMhEf0k+AR9aNVfeYjvRYfvXgMV1pMTQLKWAhD0wEuHny9eO Be/g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=RSVPYpp1ByIX+MOdPLR+WqEBg5BdEHD2ys5Dwm3oOIA=; b=SDyZg2UeBrb2Aw3VqAjSybZRGDWEpk+uRmL5H6nI7w3yjJZZCprw1ey+/VXGBk8666 iAe+u+b8t838nNu7+RafXbsZ+RK5XfySzKoR2dmrhO2bR3ZMHh35r7TntbSVLZRUHIbE KB66h7tBP0Gq2c9/rD3M2fSXg5k8atDkVKXJyzX+FfB2+LwekxZKT0e4Y1573RJzMRdo LNuq+eG8E4fbQYaBC8T7sPo57MySvM15tU8uRfy5V4cTQ8SNrZE/zi4eMdwMWfZbn2c3 3kT5tlYj7+aCAsuvnDWxZ6e/sUwhZAKe89HxIX8a7o4X0Y+j+xLEFaqdjkGwviVOPO9S UMRg== X-Gm-Message-State: AOAM533BbYUTY7KgK6q5dK8aCYmfV2i+w8QdQdEqlhTOapVulbr7c9Uu 27MQ7xzV+R1L0QiORUS1udDUbW5MCwU= X-Google-Smtp-Source: ABdhPJx5iq4zn1R8NiglR4QyX0bQTdvRTeWZ7Q7d+l8vfiC3g8YsoAZO9Dmo+P3/K7LP5i2wXR1V5Q== X-Received: by 2002:a05:6000:18c3:b0:206:1575:ec8f with SMTP id w3-20020a05600018c300b002061575ec8fmr14565176wrq.479.1649430004653; Fri, 08 Apr 2022 08:00:04 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t185-20020a1c46c2000000b0038e7092025bsm10388554wma.20.2022.04.08.08.00.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 08:00:04 -0700 (PDT) From: zimoun To: 54790@debbugs.gnu.org Subject: [PATCH 3/3] gnu: Add r-copykat. Date: Fri, 8 Apr 2022 16:59:54 +0200 Message-Id: <20220408145954.3345224-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220408145954.3345224-1-zimon.toutoune@gmail.com> References: <20220408145954.3345224-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54790 Cc: zimoun 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 (-) * gnu/packages/bioinformatics.scm (r-copykat): New variable. --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 106b25a50b..e3cca9aab8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9138,6 +9138,44 @@ (define-public r-cellchat communication networks from scRNA-seq data.") (license license:gpl3)))) +(define-public r-copykat + (let ((commit ;no tag + "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53") + (revision "0")) + (package + (name "r-copykat") + (version (git-version "1.0.8" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/navinlabcode/copykat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8")))) + (properties `((upstream-name . "copykat"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-dlm + r-gplots + r-mcmcpack + r-mixtools + r-paralleldist + r-rcolorbrewer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/navinlabcode/copykat") + (synopsis "Inference of genomic copy number from single cell RNAseq data") + (description + "This package Copynumber KAryotyping of Tumors infers genomic copy +number and subclonal structure of human tumors using integrative Bayesian +approaches to identify genome-wide aneuploidy at 5MB resolution in single +cells data. It separates tumor cells and tumor subclones from normal cells +using high-throughput sc-RNAseq data.") + (license license:gpl2)))) + (define-public sambamba (package (name "sambamba") -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 11 10:14:56 2022 Received: (at 54790-done) by debbugs.gnu.org; 11 Apr 2022 14:14:56 +0000 Received: from localhost ([127.0.0.1]:44882 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nduoi-0008Sc-13 for submit@debbugs.gnu.org; Mon, 11 Apr 2022 10:14:56 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21004) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nduof-0008SS-EU for 54790-done@debbugs.gnu.org; Mon, 11 Apr 2022 10:14:54 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649686490; cv=none; d=zohomail.com; s=zohoarc; b=iOWU0s5kZFwpPGkQb20PH8ttJj3Vk2ZEd5EI24Zf99dHjAIE3MVSS2zNE5QD1ZDuraR85wi8OGLdixz7RIxGA5PDWsr4DIuE2sVIJL/d0IjvXP5XF4oWsI+O/lJC0ABjdg8JesMw5u+pkm+PXrQjANS7h4l1dTgxChhluyCXXX8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649686490; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=4OZQM1JUt28/Vy95pZUVUs798UyZ5+3OkyqlYVutFy8=; b=Uw9cPgxBkdG4FX9RFjUhkxUUqGp3jBGive6OGLsC1wziJiYC6HyClvDG2axhwgdLKuIz5POLEjtvnhnEVKzzo6kCwg1hEiwelzKh+nLotQy7UoA3Olmf7gNSBPoOJFw0uhiQ1scEZiFjnVtIpnmGQvM7XoTujxAq2tgnyYq5NKc= 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=1649686490; 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=4OZQM1JUt28/Vy95pZUVUs798UyZ5+3OkyqlYVutFy8=; b=h6YRTZYeLBbQzNg5Z5FjPXwBIWa/RaVCPiSGFO6CbI2opb7k+z9qWsp8Y3Krquh1 go7JgbGXJDXCVxvfCcSN7igk3mt3IhTevuk1wVA9/+h0Mpk1IcLSoUKw5B7BaJn3D2F Sa1TsLQVZWpJSzq48NCInophFbZ1LhbmdSjHHVng= Received: from localhost (i5E862D75.versanet.de [94.134.45.117]) by mx.zohomail.com with SMTPS id 1649686480364848.230740826389; Mon, 11 Apr 2022 07:14:40 -0700 (PDT) References: <20220408145829.3344728-1-zimon.toutoune@gmail.com> User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#54790] [PATCH 0/3] Add r-copykat and dependencies Date: Mon, 11 Apr 2022 16:13:22 +0200 In-reply-to: <20220408145829.3344728-1-zimon.toutoune@gmail.com> 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: <878rsbzoz7.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54790-done Cc: 54790-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 (-) Thank you for the patches! > zimoun (3): > gnu: Add r-paralleldist. > gnu: Add r-dlm. > gnu: Add r-copykat. I shortened the description of r-paralleldist and pushed the three patches. -- Ricardo From unknown Fri Jun 20 07:26:16 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 May 2022 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