From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:04:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.160874663912162 (code B ref -1); Wed, 23 Dec 2020 18:04:01 +0000 Received: (at submit) by debbugs.gnu.org; 23 Dec 2020 18:03:59 +0000 Received: from localhost ([127.0.0.1]:54057 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8UQ-0003A6-Vc for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:03:59 -0500 Received: from lists.gnu.org ([209.51.188.17]:34028) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8UO-00039x-CT for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:03:57 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56266) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ks8UO-0001Jb-7A for guix-patches@gnu.org; Wed, 23 Dec 2020 13:03:56 -0500 Received: from mail-wm1-x32a.google.com ([2a00:1450:4864:20::32a]:38725) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ks8UM-0000JT-JA for guix-patches@gnu.org; Wed, 23 Dec 2020 13:03:56 -0500 Received: by mail-wm1-x32a.google.com with SMTP id g185so190390wmf.3 for ; Wed, 23 Dec 2020 10:03:54 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=CSQWs/RwKhPbNk4OKKfU3SNdZr6jiTdKVhKpCQqE4VI=; b=uYeI8gNdAXY6zwxDq86YKSoSRmgs6ye93ccCnY+QcupTVnbAVhe2HQvDaV9uuJ379p CoVY+/KP42xxvV3G8BBy8iXcH4cQSFItZstcEHnX2QnexkQlL/GnXbuJ07oezosmgd0J gRb6ci4WvecVCcBQxwLIjRPd1Hu584rx/F0+kgRLWTSVCuOfTfUuaQlr0Jmie4mBCtwK APny4cTK8BzGMHXeEL5ZTn2zYZhaHo50CAWBKQAsXA8ze3WGlLGv/G6FoBxeYkrUk9sl jMg35xW7NzFSUa2/BwAwMHk99fqgrJObrfZI/fYC+h8mgzA/cdl/wifpDVcoCAa70xMv +YAQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=CSQWs/RwKhPbNk4OKKfU3SNdZr6jiTdKVhKpCQqE4VI=; b=sGsbmNuOqXmlBAd74mPDRBOzp3kIcaVDrnNJBFMqv8qBe+CN8zPf+nyLCxwc9UDMQ1 DA6uCAMr+Vj5vFjuN5S/+Kvi18Ab+w1LduCe8+GRKCySqx/LnAuZdj2uwLCb2CMO4sm3 2rKVYTMnZQFK9OQYkoFqPJ31iuOAjYZyr71yWGIRlaeIezQ84+QrpWxapBo1F7zqtD4M OsFuGRKQ2IaP7t8+Ul4toTpGNCSFaEmyJfaMkll+TjS5gft2heqf0Vm2EQWPyxyBzxFT zpRrJnLXGdZDeVthAblOt3//oU97+aoxq7zHC9IGOvwVIoQdq/eqD74aSUcV+GS8xvfq Z6gg== X-Gm-Message-State: AOAM530NGzz6JsR78jAA2lskguAUE2mW8MtAfrK2PrqiCbA550BhVsna AV2mxHRP/9d797yp3psKcg6GXmlCzjw= X-Google-Smtp-Source: ABdhPJw2kdFErSPo6O6UPHctWfA1FKhnLO8X0eKTfZ9o/ocwVWPGWwJXFz6gRIdEiaXKdDBif3t4Pw== X-Received: by 2002:a1c:b742:: with SMTP id h63mr820871wmf.122.1608746632923; Wed, 23 Dec 2020 10:03:52 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id h5sm37512466wrp.56.2020.12.23.10.03.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:03:52 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:03:38 +0100 Message-Id: <20201223180338.58588-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::32a; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32a.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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) 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, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). Far to be complete; still 7 pacth set like this one are coming... 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- Then, after the move, I run: ./pre-inst-env guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check and at the end of the series, I run: make as-derivation to check that "guix pull" is not broken; just in case. Last, I have not carefully checked the imported modules, so it could be possible to perhaps remove couple of #:use-module (gnu packages ) in gnu/packages/bioinformatics.scm. All the best, simon zimoun (10): gnu: r-sushi: Move to (gnu packages bioconductor). gnu: r-gwascat: Move to (gnu packages bioconductor). gnu: r-gviz: Move to (gnu packages bioconductor). gnu: r-gqtlstats: Move to (gnu packages bioconductor). gnu: r-ldblock: Move to (gnu packages bioconductor). gnu: r-erma: Move to (gnu packages bioconductor). gnu: r-homo-sapiens: Move to (gnu packages bioconductor). gnu: r-snpstats: Move to (gnu packages bioconductor). gnu: r-gqtlstats: Move to (gnu packages bioconductor). gnu: r-ggbio: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 400 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 405 -------------------------------- 2 files changed, 400 insertions(+), 405 deletions(-) base-commit: 4994e1f2bd9b573d2c13abf2b98ec204f510ad11 -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 01/10] gnu: r-sushi: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874680612505 (code B ref 45399); Wed, 23 Dec 2020 18:07:02 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:46 +0000 Received: from localhost ([127.0.0.1]:54077 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X7-0003FR-Oh for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:46 -0500 Received: from mail-wr1-f52.google.com ([209.85.221.52]:34286) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X6-0003Ey-DB for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:44 -0500 Received: by mail-wr1-f52.google.com with SMTP id q18so86798wrn.1 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:44 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=Hn2j79csnCCVkNW9aAShcYd0i2dYpBduKK6LIydG+aY=; b=dA1NNgN2yzxg0XmFJkMscm0B/JfhFmryTBdOLu+2YTYAqrnfwFYvNSr2DTiJJlGpZe m+cEW8a14C4tuvR2YHg/PAUv5c1Bz3LqKbyj4shsi3kOy+RLMjg47TpmnTa5EGw2qeC3 TSin+qqB51+2gC2t6waCAzEiJkajcYSB0BEz78+tAU203SHgtqBBMbF61pAKR2WH0IPW xyO5/KpnNkPVfdbDhpxHeMu00BCf49W5NVEMrCaORGthSWTY+mx+WlT0GZphx2cebFAv I8BIUxjf+mz+S0CH+BJ5NV60a6q2eBixF6zgTndLq2XXH8F9/J6quAaU8B6yX5Vdg2fG ky4A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=Hn2j79csnCCVkNW9aAShcYd0i2dYpBduKK6LIydG+aY=; b=OqcRDom3JnLAmiZBjR2bUq67dooLUqmDOs8agykMyEoouzadKqim7MXeqasg5nLKzb pmIBDxxrBhhj4D1or24K/B6P4C/fuHDK+XpEmgUM4ejQwoPRj7zF/5hByE0t5LSwM6Xs J2utRd8fG+8BcU8INkLhD9HibelXuCbgpOuerCi5VBH8eAXEoL/OysqZjFnfI94OVGo+ KHQgiM605kzezVT4G/30Rak3sHz/vNFnqJPZy1YxavDPd/t6oEyzBh6xM/ZJ6aLdwMML SHMEovuXpKnXm0ipWJmbxXeeq6miscrGE1n5YhvktOWC4VE29rcMIJhuDq7dglpRflxa g3kQ== X-Gm-Message-State: AOAM531wKwVaZ0In6kzTdwyYz+1Rm/zBMXQW8UeTG2XUJXxdGlClWDPh 3Mkj6u6w6dPerAEDVcmnkghhY31wPk4= X-Google-Smtp-Source: ABdhPJzI6D2nph714LSZf/4HFUwXtotX4WgO2vCAUcASe16Ss7k4wVuBBl5Fgr76ULFl0QQI9auXXQ== X-Received: by 2002:adf:f891:: with SMTP id u17mr30958273wrp.253.1608746798914; Wed, 23 Dec 2020 10:06:38 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:38 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:26 +0100 Message-Id: <20201223180635.58647-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-sushi): Move from here... * gnu/packages/bioconductor.scm (r-sushi): ...to here. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 22 ---------------------- 2 files changed, 22 insertions(+), 22 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 33f66ce8be..3dd34e7f24 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9300,3 +9300,25 @@ graph with the mapped data. In addition, @code{r-pathview} also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+))) + +(define-public r-sushi + (package + (name "r-sushi") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Sushi" version)) + (sha256 + (base32 + "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) + (properties `((upstream-name . "Sushi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biomart" ,r-biomart) + ("r-zoo" ,r-zoo))) + (home-page "https://bioconductor.org/packages/Sushi") + (synopsis "Tools for visualizing genomics data") + (description + "This package provides flexible, quantitative, and integrative genomic +visualizations for publication-quality multi-panel figures.") + (license license:gpl2+))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 96fa22f1a3..6ef93d9b62 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10867,28 +10867,6 @@ with your data.") EMBL-EBI GWAS catalog.") (license license:artistic2.0))) -(define-public r-sushi - (package - (name "r-sushi") - (version "1.28.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Sushi" version)) - (sha256 - (base32 - "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) - (properties `((upstream-name . "Sushi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biomart" ,r-biomart) - ("r-zoo" ,r-zoo))) - (home-page "https://bioconductor.org/packages/Sushi") - (synopsis "Tools for visualizing genomics data") - (description - "This package provides flexible, quantitative, and integrative genomic -visualizations for publication-quality multi-panel figures.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). References: <20201223180338.58588-1-zimon.toutoune@gmail.com> In-Reply-To: <20201223180338.58588-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874680712512 (code B ref 45399); Wed, 23 Dec 2020 18:07:02 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:47 +0000 Received: from localhost ([127.0.0.1]:54080 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X8-0003Fe-JJ for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:46 -0500 Received: from mail-wr1-f51.google.com ([209.85.221.51]:35040) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X6-0003Ew-4h for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:45 -0500 Received: by mail-wr1-f51.google.com with SMTP id r3so78463wrt.2 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:44 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=CSQWs/RwKhPbNk4OKKfU3SNdZr6jiTdKVhKpCQqE4VI=; b=WzQKtm9USwxhir5HQeZCKTKAU10elYvIzl6hbkb6frhIUjtIW9nBtQFytjympPZCjt U32/7N1tTFS+0JnniyCpZLY5VpUgXVk8TNYlIwZTHvAIDJiuBTBrFO7z3rHEv1jbLguH axxPfaow2SMvV4k63jqPR+HxNjLQ4ppHdSK/Xx/Kze0vF5knlhz7l05q2hhwaJSuB5+R rvBqkKgY1fYBTuCtYF6RT+5dXToC7wDAwS3iieg/P2lEbLdDgOtful4hWvSSAevr/zJh DbShwJg2qrO3tiiZIfQvdPJBEzqN2Mpl8D/zaQ/eVXFEp0fESMQynkwL0W4xy5YtkkYR DSLw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=CSQWs/RwKhPbNk4OKKfU3SNdZr6jiTdKVhKpCQqE4VI=; b=LL6ynFgvTz6PUxUC76kOqHnyk+Cj0bwE5UEhbgbh9z8wgDNbw0/OFqOv+SdLCbrCBM RGC2d6csUxIconAcUZznhyfRu4K++DYnRoNqPseEbRrhKMdPRM/Uf/fXo/mS43lKmBpn R8QYhcUEcmMrElzsiH37H6O886BuFjSY2KwR12ly7XUgJzLPZG2IiIKUvYwiiFYH4kkZ apQwc9uenNy8wMVNOJ9yjjuOLn3Hh+X0PGM4focxjVvNbeNS1CIQ8FUgpI544yF3+ghp V91MRyW/owi9jLxTqGfQKMVSCLeCCrsQQQPvAjni2LSW2qLqI2X9ESNvHcQ6IxDQYGRD ChLA== X-Gm-Message-State: AOAM5302H5Q31CSHF0DJks+FR2Ngv/C4P80E4rzf52hc6eOLmEppo/fc LMcTPgcGUkH67yl+Z+oBkbv3yY/0kpw= X-Google-Smtp-Source: ABdhPJzwrZz5a+zUhw6DHF8iCdwDNRJNfGWjU/BGHwdF5Jgl2xsPs5io1V1RXfYDMi3o8IVdPNXiHQ== X-Received: by 2002:a5d:4d50:: with SMTP id a16mr29870937wru.43.1608746798372; Wed, 23 Dec 2020 10:06:38 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.37 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:37 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:25 +0100 Message-Id: <20201223180635.58647-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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 (-) Hi, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). Far to be complete; still 7 pacth set like this one are coming... 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- Then, after the move, I run: ./pre-inst-env guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check and at the end of the series, I run: make as-derivation to check that "guix pull" is not broken; just in case. Last, I have not carefully checked the imported modules, so it could be possible to perhaps remove couple of #:use-module (gnu packages ) in gnu/packages/bioinformatics.scm. All the best, simon zimoun (10): gnu: r-sushi: Move to (gnu packages bioconductor). gnu: r-gwascat: Move to (gnu packages bioconductor). gnu: r-gviz: Move to (gnu packages bioconductor). gnu: r-gqtlstats: Move to (gnu packages bioconductor). gnu: r-ldblock: Move to (gnu packages bioconductor). gnu: r-erma: Move to (gnu packages bioconductor). gnu: r-homo-sapiens: Move to (gnu packages bioconductor). gnu: r-snpstats: Move to (gnu packages bioconductor). gnu: r-gqtlstats: Move to (gnu packages bioconductor). gnu: r-ggbio: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 400 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 405 -------------------------------- 2 files changed, 400 insertions(+), 405 deletions(-) base-commit: 4994e1f2bd9b573d2c13abf2b98ec204f510ad11 -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 02/10] gnu: r-gwascat: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681312563 (code B ref 45399); Wed, 23 Dec 2020 18:07:03 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:53 +0000 Received: from localhost ([127.0.0.1]:54088 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XF-0003GX-1i for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:53 -0500 Received: from mail-wr1-f43.google.com ([209.85.221.43]:35034) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X6-0003Ez-Th for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:45 -0500 Received: by mail-wr1-f43.google.com with SMTP id r3so78519wrt.2 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:44 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=6u98ShJItMSRCuJDF7f1vxJo+6zTOsfZ4RHre4E4fD4=; b=KdGg/qEtcikDOJzZLyx+iJxukWNK+vu/PCZI+sG320FQaceBa7Xzk6pmetJNxYfjr/ nOGyt/aqd3XVEsFr00NfOoAIkqqiqqlmK95pLFxB91a+dbaf/3/yRfvE9hafWwCPS3O7 CimIkPXPCpwUJqEaNmqAPfECHVbdPD5YMD3/njaktqIoLlvPEYDTxLnfUyzCHtNZZpJw wYVVoRvVput5JOaci2Jez5EEWWl97X3CcFP+lPwwDcKnPl16YJFWbc40hr3UMJCGPbQs yLRSltcHz5V6BoSDpGH1vI1VwArkrnCec5GcNQsRDPhgVMY+ZPJD95bkllDsAwK5YQp7 rBWQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=6u98ShJItMSRCuJDF7f1vxJo+6zTOsfZ4RHre4E4fD4=; b=fJ1SdFc8jlRojsWScea/3SOujbiGq0SYPmgXG9aflvYfCGlMHTcygyLKxWR8rh2ZXM kkqK8ThZL4QigxnAOOCApC3UQMz4GO7cJWXfNZztpFra5/5bI1KsElbxWMz9MT/deEen s7P/a615YuYkr6UrJl0qxl7Ox+vlDjzXFA1P5xF3WEU51I6H21J0/ewBJXU3yG8rzL7s EB04wFZKS5PRQEKv3vQfhwfoNHtCc/mgIecUm2iMC6G2NU27C6vN37A0IHs8b1lqsTC4 z8Yzr/vs2DmjJEvI78iWGlcD4Tm0ql1LNOgrofwO5wMlaWDKBSrLYeB3ltak16XO7EuR 2ymA== X-Gm-Message-State: AOAM532OufBFauWCgjZGe3V557SwPkF3xQ0Er15t7TPKvY7bq3BsEhQg 9Pls9eHRc97An4LJ5ZRprktURCqwydI= X-Google-Smtp-Source: ABdhPJwzvs5DGgAW+7+dyIpu+b50BDBPAoUOrict96Jw0A/ZW/0h0B15C3wABlAL8iNjyND9ed+Xow== X-Received: by 2002:a5d:61c4:: with SMTP id q4mr30678231wrv.304.1608746799430; Wed, 23 Dec 2020 10:06:39 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:39 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:27 +0100 Message-Id: <20201223180635.58647-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-gwascat): Move from here... * gnu/packages/bioconductor.scm (r-gwascat): ...to here. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 33 insertions(+), 33 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3dd34e7f24..970602a32b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9241,6 +9241,39 @@ preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (license license:gpl2+))) +(define-public r-gwascat + (package + (name "r-gwascat") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gwascat" version)) + (sha256 + (base32 + "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-readr" ,r-readr) + ("r-s4vectors" ,r-s4vectors) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gwascat") + (synopsis "Tools for data in the EMBL-EBI GWAS catalog") + (description + "This package provides tools for representing and modeling data in the +EMBL-EBI GWAS catalog.") + (license license:artistic2.0))) + (define-public r-kegggraph (package (name "r-kegggraph") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6ef93d9b62..ab187dcddd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10834,39 +10834,6 @@ grid graphics package. This results in genomic information plotted together with your data.") (license license:artistic2.0))) -(define-public r-gwascat - (package - (name "r-gwascat") - (version "2.22.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gwascat" version)) - (sha256 - (base32 - "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-s4vectors" ,r-s4vectors) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gwascat") - (synopsis "Tools for data in the EMBL-EBI GWAS catalog") - (description - "This package provides tools for representing and modeling data in the -EMBL-EBI GWAS catalog.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 03/10] gnu: r-gviz: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681412570 (code B ref 45399); Wed, 23 Dec 2020 18:07:03 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:54 +0000 Received: from localhost ([127.0.0.1]:54090 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XF-0003Ga-Er for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:53 -0500 Received: from mail-wr1-f50.google.com ([209.85.221.50]:34286) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X7-0003F1-Gz for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:46 -0500 Received: by mail-wr1-f50.google.com with SMTP id q18so86845wrn.1 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:45 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=9az8tytk2QNrhEUiQmiHQtFE9X1nBcpZ5oHK4efU/ck=; b=YzwfJIa0aSXPOY5X+S6mni2bMTZ8zbUwhhKHD4jq0O+1KZHT/CS+KrKC4mE2gAB8Xw ipNBVoInc3lsWgL/kuGDeRsI3A16prpXKZLxCq6/2uZT0FAoUOya7rstiWpP2DDxLlA1 lUOsnCyDjA8cXr1asyDr5CXw8ezZdRqOiTJvlXFzKHrizyhPl6yj6BHbvAdXFvyOlY/K wxqa+M0Am97BYovXjHpOcB/rzntgu80rscUl6xqgffxnnZlmBv7b7bv9MH7o3Y0woBCl 9HRfGwWz4L+CM5fpVsUxAuI50b3Z0lKToRgH/95lhaKuT3uvkbzEKIpi9dgziT/VbUtU EUYQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=9az8tytk2QNrhEUiQmiHQtFE9X1nBcpZ5oHK4efU/ck=; b=l0xnZzG1McrTypy8s9D9+oQYREehI1jmKqMQDDTjFp4SS5FYMBRZDl1R8SKyS2GoIQ GXxhiw63FSWJINCfGEPaqu578D5uyE82d13fYCLvPtXFwnuVoOetOlNJBE8zJGWCWR7K Gf+rneovHpzcj9hlxlufJgD3RoMi3e0yN0+g3vk7HakJX65F5lzLn9Y99xYiIImio9Pw G3Py0RI31S0qJCR1lzadubMlnmACv2Yh94xLUMOgbYwlvtqacc+ZQh21l5QRWvNn2GEA sSIKsYVtkkgXn+RM7gHEKySaArJSAeNGDWp1myf828AmHHh5XSX1XBjRpHHy0pWv8PtR DFsw== X-Gm-Message-State: AOAM530qdFvyNy642+qhbvD2n+Mn3Da9P/fpZxXSCZAvHCtJYTpULis7 AGcV68gjydltjuodgzu1Z9lBfa3m/Zk= X-Google-Smtp-Source: ABdhPJwRyKveCk6NbaMkWNquXMKi8NJ63DRADwxmU6BmDrtRfePu6diQx7UwgQl/xJby2kKjcsGTrA== X-Received: by 2002:adf:ea45:: with SMTP id j5mr30724148wrn.171.1608746799978; Wed, 23 Dec 2020 10:06:39 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.39 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:39 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:28 +0100 Message-Id: <20201223180635.58647-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-gviz): Move from here... * gnu/packages/bioconductor.scm (r-gviz): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 --------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 970602a32b..11e9a46b11 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9241,6 +9241,55 @@ preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (license license:gpl2+))) +(define-public r-gviz + (package + (name "r-gviz") + (version "1.34.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Gviz" version)) + (sha256 + (base32 + "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) + (properties `((upstream-name . "Gviz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-digest" ,r-digest) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Gviz") + (synopsis "Plotting data and annotation information along genomic coordinates") + (description + "Genomic data analyses requires integrated visualization of known genomic +information and new experimental data. Gviz uses the biomaRt and the +rtracklayer packages to perform live annotation queries to Ensembl and UCSC +and translates this to e.g. gene/transcript structures in viewports of the +grid graphics package. This results in genomic information plotted together +with your data.") + (license license:artistic2.0))) + (define-public r-gwascat (package (name "r-gwascat") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ab187dcddd..caa505fdab 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10785,55 +10785,6 @@ interpretation of members of a collection of association statistics on a family of feature/genome hypotheses.") (license license:artistic2.0))) -(define-public r-gviz - (package - (name "r-gviz") - (version "1.34.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Gviz" version)) - (sha256 - (base32 - "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) - (properties `((upstream-name . "Gviz"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-digest" ,r-digest) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/Gviz") - (synopsis "Plotting data and annotation information along genomic coordinates") - (description - "Genomic data analyses requires integrated visualization of known genomic -information and new experimental data. Gviz uses the biomaRt and the -rtracklayer packages to perform live annotation queries to Ensembl and UCSC -and translates this to e.g. gene/transcript structures in viewports of the -grid graphics package. This results in genomic information plotted together -with your data.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 04/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681412578 (code B ref 45399); Wed, 23 Dec 2020 18:07:04 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:54 +0000 Received: from localhost ([127.0.0.1]:54092 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XG-0003Gh-0L for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:54 -0500 Received: from mail-wr1-f41.google.com ([209.85.221.41]:43765) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X8-0003F2-6W for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:47 -0500 Received: by mail-wr1-f41.google.com with SMTP id y17so33402wrr.10 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:46 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=gpB9Px+cqqf/Thjv5v3FF4iUPRufvKc0i7Qw1q4Y8TA=; b=aOXGU8UoyA8PHCZ+KuQskDipE9tBjg61pewuFEY0nBdhD0R9NkVgvgwkiHdQ9kf2jB F1G4lUvT5XHXlctdXzf4SRFs79wkLUBiSpAs0XqOpEByZCSbzJhgBbKrfoI9yDtj4T7j kMSp3ZTrRQDT4O6qgtKCNTRKi5zNiZOC+7AU4sVYTGFgjmuf0yUcA7SCSOfbLkEvnTJ2 gEcP5Wl/07aluqN8W8f9zycjw3ztsXqN4+GJ/YbzjTv2LCDOFWXaWQEc1z2epBijTaZW pJuyccHii7Z4EiTSYFkXK2BdhC8lQUtbfeCEwKkMe8AlVcfp8ohbjqbmHZedS/HfOqPH UU8Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=gpB9Px+cqqf/Thjv5v3FF4iUPRufvKc0i7Qw1q4Y8TA=; b=Cwg9Sc4Qghel3d1yLwiJK/HZBZMeISxjm+JAJ1vF14T0Kv6D3vQuOE1L4e69N7rovr 9A3vNjtr/xcHuBw93BySq8hIaJhk42yT/CW0jDXeyYGbhaCIlej7nUtow/atvKeIfTYw 73PylUN1uLSQeOEl9aqaZhRVZdHTX/NH7giL0jTP86ZNX2BUS7NUTiJCm2cahM7qGjA0 LHGeaY2JdsOPAJRRpDROLo+iUbO+rVfvjaRNuYutRXjyMJQ6Y/XpYrQYqz7PnTPiL7Fh Y8TTLME7EzQa8++hmcUPAFkfH4YF+tJxKFletapkD7EIKdVGvMpMZJeGJVxeeFUCkX/J ClMQ== X-Gm-Message-State: AOAM530bKXLyoJMKOXk+TXxGrfKEyGM/aGnh7NrRp6ZMS+tvZdmvL09J Lzpv4qDvHFRcVWaB4J09bbVp4HJyPi0= X-Google-Smtp-Source: ABdhPJy035YJHwhB6jXSxVYQIxOR3LLaCwnJU6rnsRtQZRpgCVoltkpOtbab5YoyNsQNI/XZ0jlP6g== X-Received: by 2002:a05:6000:1d1:: with SMTP id t17mr31495984wrx.164.1608746800645; Wed, 23 Dec 2020 10:06:40 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:40 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:29 +0100 Message-Id: <20201223180635.58647-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here. --- gnu/packages/bioconductor.scm | 56 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 56 --------------------------------- 2 files changed, 56 insertions(+), 56 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 11e9a46b11..1bf9a49272 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9241,6 +9241,62 @@ preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (license license:gpl2+))) +(define-public r-gqtlstats + (package + (name "r-gqtlstats") + (version "1.21.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLstats" version)) + (sha256 + (base32 + "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) + (properties `((upstream-name . "gQTLstats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-batchjobs" ,r-batchjobs) + ("r-bbmisc" ,r-bbmisc) + ("r-beeswarm" ,r-beeswarm) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-doparallel" ,r-doparallel) + ("r-dplyr" ,r-dplyr) + ("r-erma" ,r-erma) + ("r-ffbase" ,r-ffbase) + ("r-foreach" ,r-foreach) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbeeswarm" ,r-ggbeeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-gqtlbase" ,r-gqtlbase) + ("r-hardyweinberg" ,r-hardyweinberg) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-mgcv" ,r-mgcv) + ("r-plotly" ,r-plotly) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-snpstats" ,r-snpstats) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gQTLstats") + (synopsis "Computationally efficient analysis for eQTL and allied studies") + (description + "This package provides tools for the computationally efficient analysis +of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. +The software in this package aims to support refinements and functional +interpretation of members of a collection of association statistics on a +family of feature/genome hypotheses.") + (license license:artistic2.0))) + (define-public r-gviz (package (name "r-gviz") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index caa505fdab..67b4c4cb73 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10729,62 +10729,6 @@ handling of existing population-level data for the purpose of flexibly defining LD blocks.") (license license:artistic2.0))) -(define-public r-gqtlstats - (package - (name "r-gqtlstats") - (version "1.21.3") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gQTLstats" version)) - (sha256 - (base32 - "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) - (properties `((upstream-name . "gQTLstats"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-beeswarm" ,r-beeswarm) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-erma" ,r-erma) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gqtlbase" ,r-gqtlbase) - ("r-hardyweinberg" ,r-hardyweinberg) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mgcv" ,r-mgcv) - ("r-plotly" ,r-plotly) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-snpstats" ,r-snpstats) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gQTLstats") - (synopsis "Computationally efficient analysis for eQTL and allied studies") - (description - "This package provides tools for the computationally efficient analysis -of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc. -The software in this package aims to support refinements and functional -interpretation of members of a collection of association statistics on a -family of feature/genome hypotheses.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 05/10] gnu: r-ldblock: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681512585 (code B ref 45399); Wed, 23 Dec 2020 18:07:05 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:55 +0000 Received: from localhost ([127.0.0.1]:54094 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XG-0003Gp-Ge for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:54 -0500 Received: from mail-wr1-f46.google.com ([209.85.221.46]:39412) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X8-0003F4-P3 for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:47 -0500 Received: by mail-wr1-f46.google.com with SMTP id c5so56923wrp.6 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:46 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=NQVz4PGBrq30qwSd+pzGw+tOaP28UlU65BqF4lByx74=; b=TSgVoLqX0P6zBE6pHULlq7C93iWCx+4s5JIRa9KWuRzjBK7BxG6/D18en8K3Mqg5Ce LL54JsiMOos/Cy46c5/4SxXR5gKvOHBBjk7ABgLw7f38jSNudiF0lXEaN2DCRmevTzfQ ekRxxxy2R3uOnkc6rZP4JeUtOQ+CqHBNq0l7q92hdw1ENqTpjrvr+QvSWFPkHdk06s16 NLar6bKArZgqXCIn1Wa5+SswLpvOyNKwKJ6zGz4EP4n/n7Mr+RFfZ3ijIokv2ljKm7P+ 37zqe83JCDayu2RSuXD2zhEwWvSpJ3ZeC2e+eHwWosqOfLQxzRBm/OmtDQoD23wzkkvy tzTQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=NQVz4PGBrq30qwSd+pzGw+tOaP28UlU65BqF4lByx74=; b=nfUdmcNt4Lj59eCYcx6SyfmSVnQtACmnctpIpr3o3JVa+jWy2sCF0TSdQQ2hGh3QTl fZUO9IGU6EEzD2t8z57zZzURmbW5/yiKwPvLs41VLdNyKsV8OwTqfrwIzg4DXiHNlDa4 YDwGi78wtisWmrsxaSevJ56U86+7vsS1Rc9q5adPZIr6eVSvSavxEJBCQsoR3hJL6PVq 5niAjuttqWeT4uyCeqgFfymtRX1Qz/ecQnOBkpPvyO7Wvcg6PyjZpwIWljAj4EqWaP1N P/sn3g/2pjBHzMqvNsGO/R4p2Hv5QWGP3ILR+gY+B3L1aDOUo+X9+XLvHJ5FlWjx9jMz tSKg== X-Gm-Message-State: AOAM532rqzKJURlZkfyI0LHsBzE2c9q6O5t3c1IVc7eG7nZ7mmuMJIFj a/vBSp8KDuKwgEUvX3T1VT+D6xd8mqw= X-Google-Smtp-Source: ABdhPJwGH/+nz4L+6GTTtIteu1HJALi49vT8BxBG5iC8IJzhfB3dU2rNzbwPBTf3WBCD+6r0oItNFA== X-Received: by 2002:a5d:50c3:: with SMTP id f3mr30364364wrt.287.1608746801240; Wed, 23 Dec 2020 10:06:41 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:40 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:30 +0100 Message-Id: <20201223180635.58647-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-ldblock): Move from here... * gnu/packages/bioconductor.scm (r-ldblock): ...to here. --- gnu/packages/bioconductor.scm | 34 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 --------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1bf9a49272..40a02dbe7f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9405,6 +9405,40 @@ maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.") (license license:gpl2+))) +(define-public r-ldblock + (package + (name "r-ldblock") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ldblock" version)) + (sha256 + (base32 + "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfiles" ,r-genomicfiles) + ("r-httr" ,r-httr) + ("r-matrix" ,r-matrix) + ("r-rsamtools" ,r-rsamtools) + ("r-snpstats" ,r-snpstats) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/ldblock") + (synopsis "Data structures for linkage disequilibrium measures in populations") + (description + "This package defines data structures for @dfn{linkage +disequilibrium} (LD) measures in populations. Its purpose is to simplify +handling of existing population-level data for the purpose of flexibly +defining LD blocks.") + (license license:artistic2.0))) + (define-public r-pathview (package (name "r-pathview") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 67b4c4cb73..25021f1ee8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10695,40 +10695,6 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.") (license license:artistic2.0))) -(define-public r-ldblock - (package - (name "r-ldblock") - (version "1.20.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ldblock" version)) - (sha256 - (base32 - "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/ldblock") - (synopsis "Data structures for linkage disequilibrium measures in populations") - (description - "This package defines data structures for @dfn{linkage -disequilibrium} (LD) measures in populations. Its purpose is to simplify -handling of existing population-level data for the purpose of flexibly -defining LD blocks.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 06/10] gnu: r-erma: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681512592 (code B ref 45399); Wed, 23 Dec 2020 18:07:05 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:55 +0000 Received: from localhost ([127.0.0.1]:54096 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XG-0003Gw-TW for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:55 -0500 Received: from mail-wm1-f49.google.com ([209.85.128.49]:34607) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X9-0003F8-GN for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:48 -0500 Received: by mail-wm1-f49.google.com with SMTP id g25so1817957wmh.1 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:47 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=ae6qp1DtyoAcVjzfzeb5MyVyAI7EI7lwggTh5Zou2kY=; b=Hr5cFx45XLHhEn/ihg1osBQykCJy8G8GcMXzWcLCYdDZu4eXcY1wGGvrSRI2m+rnx6 nPlI41TOt5Expq3IWYbrkTdlNaY93xPqotWh9sSJXYllH+Lj+zQbkZmUJWfeQ1M1xczq MPcv8nzrZys9liASrTVbMfYyXWRZ6DUgTgZKwmWn0Y9dYhIU2WEInfygANpwY/R79D3J KPXktALatkKw8eqsQKs3fI7B9BNJsvl7ANwIicgxgISdFQyhnDAhlEgXIDalc1A4U07s Cx3JOxbAmfa7rnDvG3TuiviQRpRAxcHVTnn6LnHVMOQCOiYFfcZ/gDQ0WrAA5CLeMIfi u4NQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=ae6qp1DtyoAcVjzfzeb5MyVyAI7EI7lwggTh5Zou2kY=; b=RxkRvDFZsfdZODqB7KPmtnfQzSzTsDeq2FxOoKih9GC2VJ9gjBfzG9M0dmWXCj4nhe TUU3az3IuBVbhu8oksfbRgvGmr1qBJXrIo8BXHXebZ29QkzgKR4JXrFMEQ7Xqqdhba6I +nftST+j5GNNWQILnrZAZ8pf3tO5t6OAcxGQ/3ZVekeYNDvgCRA49+pjjnaJGzW9cgH7 gsWyck33UjiNOIp4oNtIEctZKiD6UeBsopY3B3z7bcT+BBCNuuR+82XMyYulK/r8vEgY UrlBt6IZ/oCoh4rXx7NiWtxxvo73ABj6GLDp+kMGbmCKalb2VOHGrfEiJWIiXj2Qplwd RWlA== X-Gm-Message-State: AOAM530hPe/15mWwL2wNddWAdfPbquS4OQmvM8wLQf4F1MB98xcRCrjv yfcqD4oaCUlKCOQyGu+VDzEHR3o44hc= X-Google-Smtp-Source: ABdhPJxAiYYIQd6BhXj12SWbaomtXmuAndSq6mgi52qBbhQ5e6yEnlnCwZF9IHHSTeDDPRsTBq1c5g== X-Received: by 2002:a1c:2646:: with SMTP id m67mr816291wmm.81.1608746801825; Wed, 23 Dec 2020 10:06:41 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:41 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:31 +0100 Message-Id: <20201223180635.58647-7-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-erma): Move from here... * gnu/packages/bioconductor.scm (r-erma): ...to here. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 --------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 40a02dbe7f..466bb71101 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9241,6 +9241,46 @@ preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (license license:gpl2+))) +(define-public r-erma + (package + (name "r-erma") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "erma" version)) + (sha256 + (base32 + "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/erma") + (synopsis "Epigenomic road map adventures") + (description + "The epigenomics road map describes locations of epigenetic marks in DNA +from a variety of cell types. Of interest are locations of histone +modifications, sites of DNA methylation, and regions of accessible chromatin. +This package presents a selection of elements of the road map including +metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines +by Ernst and Kellis.") + (license license:artistic2.0))) + (define-public r-gqtlstats (package (name "r-gqtlstats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 25021f1ee8..1c59d7a690 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10655,46 +10655,6 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") several related annotation packages.") (license license:artistic2.0))) -(define-public r-erma - (package - (name "r-erma") - (version "1.6.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "erma" version)) - (sha256 - (base32 - "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/erma") - (synopsis "Epigenomic road map adventures") - (description - "The epigenomics road map describes locations of epigenetic marks in DNA -from a variety of cell types. Of interest are locations of histone -modifications, sites of DNA methylation, and regions of accessible chromatin. -This package presents a selection of elements of the road map including -metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines -by Ernst and Kellis.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 07/10] gnu: r-homo-sapiens: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681612601 (code B ref 45399); Wed, 23 Dec 2020 18:07:06 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:56 +0000 Received: from localhost ([127.0.0.1]:54098 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XH-0003H3-EY for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:55 -0500 Received: from mail-wr1-f49.google.com ([209.85.221.49]:41830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8X9-0003F9-Vo for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:49 -0500 Received: by mail-wr1-f49.google.com with SMTP id a12so44408wrv.8 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:47 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=peYF/DoNoLu3JFCsZndzO5YP6WEcT8mXxSok6WpQS0Q=; b=Z1xhEEuRaIxSlJWzERkYjCxDf9kj4seg1PyWwKxqeT8iyjUMjNL0kVr2DUKObDRN94 FSKl0jm0fdZsVxeLb/PMApBn3phr3LV5dWe+wBaMIzSYtFBqjL/TpiFl0gOzuazC3FGe 1231qjbWlXCkfGlkf30KAnPGr7Id2V8hnxiJ0SimwJ4k6NKV7iR7j7Vn7vGA0luC1HDJ gMBHHhdKs4VU7KY5JnmsPeMjJoctmfVKk5cIh7fb/gjeBGJEuIZ47hEGnR/aYPMUNSHy eXX9/j8w/Qyi6QzpVOz3L2yOkULy7FBwZ++0j9euiOiRfJ+JP8AUlv71/U9SSiC+krvW m+7A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=peYF/DoNoLu3JFCsZndzO5YP6WEcT8mXxSok6WpQS0Q=; b=iVuSrd3mXae4vXkz6sgiITJ+EQwKf01F9zpZY4EyL/fWuNglszCdt13hFfRgKUUpCd XDRxgbdQ4zcErYsoDLMDbJdFoOBEr2NfuwjHX/uodlwmVlT2djq7Mm4iflNyxgrFAKLP FumAs7tk4L8EvLQQhxjVsMd7ASGZ3/T030EiP/oJNw0o9zax6XGxNOjK6wRAWQ83xb0b nc9JDwOF4Vz0bAuWteKfVT5wjXXa0ZfbULXsVkka1Ed+HSwKqzifmNI3EWMYGcp5mP++ Yhf/hgdAIgR91Klqs/I+EW3pbUOzomKOlKDCvFQyK0xCx8aAw/3rNAdhVOhSu+tcge7d WoEA== X-Gm-Message-State: AOAM532rP7RWuVlUOxWz3Rhlqgtpr+hawFSPUvmjokCTCcmiA2TtOuzt MP9q/EzB8boDCQ9bZlxhXcw3Fcl0pBE= X-Google-Smtp-Source: ABdhPJxhEJvkck/aU7Rh2mTlOg/hBUxQAWIh7glJ8y4AxHWDUB0RpxwODQTz1fArFqCw1RRZfoPXuw== X-Received: by 2002:adf:8b4a:: with SMTP id v10mr30616234wra.212.1608746802438; Wed, 23 Dec 2020 10:06:42 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:42 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:32 +0100 Message-Id: <20201223180635.58647-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-homo-sapiens): Move from here... * gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here. Replace 'string-append' by 'bioconductor-uri' with 'annotation'. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 27 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 466bb71101..3b8dce30e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -389,6 +389,33 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-homo-sapiens + (package + (name "r-homo-sapiens") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Homo.sapiens" version 'annotation)) + (sha256 + (base32 + "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) + (properties + `((upstream-name . "Homo.sapiens"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicfeatures" ,r-genomicfeatures) + ("r-go-db" ,r-go-db) + ("r-org-hs-eg-db" ,r-org-hs-eg-db) + ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) + ("r-organismdbi" ,r-organismdbi) + ("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/Homo.sapiens/") + (synopsis "Annotation package for the Homo.sapiens object") + (description + "This package contains the Homo.sapiens object to access data from +several related annotation packages.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1c59d7a690..2a6ac38505 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10623,38 +10623,6 @@ and more.") the earlier snpMatrix package, allowing for uncertainty in genotypes.") (license license:gpl3))) -(define-public r-homo-sapiens - (package - (name "r-homo-sapiens") - (version "1.3.1") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "Homo.sapiens_" - version ".tar.gz")) - (sha256 - (base32 - "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01")))) - (properties - `((upstream-name . "Homo.sapiens"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://bioconductor.org/packages/Homo.sapiens/") - (synopsis "Annotation package for the Homo.sapiens object") - (description - "This package contains the Homo.sapiens object to access data from -several related annotation packages.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 08/10] gnu: r-snpstats: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681612608 (code B ref 45399); Wed, 23 Dec 2020 18:07:07 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:56 +0000 Received: from localhost ([127.0.0.1]:54100 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XH-0003HC-TK for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:56 -0500 Received: from mail-wr1-f42.google.com ([209.85.221.42]:44727) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XA-0003FB-Io for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:49 -0500 Received: by mail-wr1-f42.google.com with SMTP id w5so27997wrm.11 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:48 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=W8SbGmlvD5SUTn2HF809hS3F4V/C4IftpCzqaXVKPSQ=; b=CXkTFlRgiaMXLHOeL1QCJZYY5qlgE1GydLIDvj3HsuXzkpWKAQJJgfUjde1mUlumkK Yzg4CO0ACCBhel4nqwXP0rEfnD/qw3NzoH4B76Dlf9uWVfDYmUaZ5whI1wdC4dj0ZPqa BxGZHCWegN2B9AAy/MVx0QVNem8L93VOIeOD5FSYh4OvHEVYisYxPZJEFDLxjs0NP6zC g+kQFuAsWjV9cvMnHzQln4E4t8jIlMiuZ3vmEjqghreX5rom/GZoygERaDoJrn46mpRo n9+izzmdYUnBQ09mhL8eHJ7oHs/YIZNeEuULCZ+la1n13g9oN9yViTJ5eBzncAvbawSC bUbA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=W8SbGmlvD5SUTn2HF809hS3F4V/C4IftpCzqaXVKPSQ=; b=m8uZe2YSMunLgTKO7ZDEMz4lpxzP2zG8QMuhft6QgUdBkY/cExpFEKUB7itkcZpsFO 0on8ntq3JGhWqF8xKsVejQkZxy9PCbHJA3S7gzHDIEg12pA3ILW7fQWzk+IdpuJcojJK xF3oA6NQidMdQmk+4fcjJ4xX4xqhJYDQXJgkn+dHNmV+7OF6Fv0YM/D5rXQCIQ3GcBJ0 9ShJnnrXABT/fWTMrXSSa6hYKktJ21Z58QcpWVDtmswkAJucCVL0KKmex8GuMMY8RW3l PczRznVxCamZKQXDoCdZgyF2u9/9Nb2A2yNjfv61rVQxVru4jjO3nw+d71rbS/ee1pne w9lg== X-Gm-Message-State: AOAM532mWraGjtcwNSm2r8BxDOfHJXvrsfIk77gKfXqdkIHqS9xNEt5S E2fkYR0Tt1t9dpemqv90Xwo+KasCq0o= X-Google-Smtp-Source: ABdhPJzwVik+uDa4oUq2tgnV/s9ktXXSNdwPmhvmQsyvMBLaSXyqCVrcmDp+hQhx/0VN08gTt5akWA== X-Received: by 2002:adf:9cca:: with SMTP id h10mr30476508wre.77.1608746803038; Wed, 23 Dec 2020 10:06:43 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:42 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:33 +0100 Message-Id: <20201223180635.58647-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-snpstats): Move from here... * gnu/packages/bioconductor.scm (r-snpstats): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3b8dce30e5..ff9e26bbde 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9540,6 +9540,33 @@ integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+))) +(define-public r-snpstats + (package + (name "r-snpstats") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "snpStats" version)) + (sha256 + (base32 + "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) + (properties `((upstream-name . "snpStats"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-matrix" ,r-matrix) + ("r-survival" ,r-survival) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/snpStats") + (synopsis "Methods for SNP association studies") + (description + "This package provides classes and statistical methods for large +@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends +the earlier snpMatrix package, allowing for uncertainty in genotypes.") + (license license:gpl3))) + (define-public r-sushi (package (name "r-sushi") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2a6ac38505..76236929de 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10596,33 +10596,6 @@ of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, and more.") (license license:artistic2.0))) -(define-public r-snpstats - (package - (name "r-snpstats") - (version "1.40.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "snpStats" version)) - (sha256 - (base32 - "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) - (properties `((upstream-name . "snpStats"))) - (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-matrix" ,r-matrix) - ("r-survival" ,r-survival) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/snpStats") - (synopsis "Methods for SNP association studies") - (description - "This package provides classes and statistical methods for large -@dfn{single-nucleotide polymorphism} (SNP) association studies. This extends -the earlier snpMatrix package, allowing for uncertainty in genotypes.") - (license license:gpl3))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 09/10] gnu: r-gqtlstats: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681612616 (code B ref 45399); Wed, 23 Dec 2020 18:07:08 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:56 +0000 Received: from localhost ([127.0.0.1]:54102 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XI-0003HJ-9s for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:56 -0500 Received: from mail-wm1-f51.google.com ([209.85.128.51]:55673) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XB-0003FD-5y for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:49 -0500 Received: by mail-wm1-f51.google.com with SMTP id c124so169565wma.5 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:49 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=JIXZfPUyUUvVrjc3l7vPUDsnSQFk0ZTymAngTOU/cLg=; b=b7ufJbaOzI4V9Fw9zRYRr+akAdm3bjG1f82SFVEInWlcLuI4WPwoz+jqiAElDvzHNv Xn9Hj9+55NYfklCHQ/fB7Z6FbVZO9kTU8vOuYC/fhCHdhiwM5tRwOTFRc3VuiH05UOW+ +feYEf/0irPzqbMUVgrCOECbgvWZhEniZ9j35gzBxhfY5ksW1ECko1eDQe1llu+KaoJ1 nQukfQXNlp1UDynC1IcbgUQDPB+9BOc+G274i7lqRJENM1hf1NfkfjY+nxDSh5doEOzi lTGVBp1oYHmtcnPcHiHPYsL2pZW410NjwjMkYAm9/PHNtupYToTOobH5tZUp5voAWVqK Apvw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=JIXZfPUyUUvVrjc3l7vPUDsnSQFk0ZTymAngTOU/cLg=; b=UTQEDkWd1wP4bAn3PtaayBu27n339GdstduYVUVMaBdBGc5fQAEfz8gD3DF9LYmTsO KWhkEbMqix0vWQHPzEQlihw6AIXg4id6+tWLNXg/KgzadjWj9MUg5+itZc9+dFDFrET3 xfR595QC9M4JVzZhLre3Jh8SJ+Eu3+/1HqqYZcmpDAO1Xv9uTfLWzaJ0UYC7fZs57US0 QmIQVosbMg62bm9uZ+ImUZz/Ju+b2qet6LqWOtl+2M7a0aM461iwdvJKzoAzbBsi9Cup UgcGFYSPdU80WQYaeXWfrJ6/7A02RXNvTTukUmFWizXSv2UdQIglG3QtoZ4ZTmfZLujV JiMg== X-Gm-Message-State: AOAM531VoTfqIj2jjz1MI5ddcjVoN/Bhwn65UkKf/OEMcc+xWLvzJJic m3DGxBJ3OdtPMMoPVhcWWHRTjwjPrqg= X-Google-Smtp-Source: ABdhPJwjo8H4boqqqeFuEYrxpHpxpuKBXh9PcKDUrLCnk6H8pWK5DcbgzD6ypv2w0TEtS888Amctdg== X-Received: by 2002:a7b:cd91:: with SMTP id y17mr767072wmj.171.1608746803662; Wed, 23 Dec 2020 10:06:43 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:43 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:34 +0100 Message-Id: <20201223180635.58647-10-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 47 --------------------------------- 2 files changed, 47 insertions(+), 47 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ff9e26bbde..a3dd93e763 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9308,6 +9308,53 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.") (license license:artistic2.0))) +(define-public r-gqtlbase + (package + (name "r-gqtlbase") + (version "1.21.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gQTLBase" version)) + (sha256 + (base32 + "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) + (properties `((upstream-name . "gQTLBase"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; This is an upstream bug. + (add-after 'unpack 'fix-imports + (lambda _ + (substitute* "NAMESPACE" + ((".*maxffmode.*") "") + (("importFrom\\(ff,.*") "import(ff)\n")) + #t))))) + (propagated-inputs + `(("r-batchjobs" ,r-batchjobs) + ("r-bbmisc" ,r-bbmisc) + ("r-biocgenerics" ,r-biocgenerics) + ("r-bit" ,r-bit) + ("r-doparallel" ,r-doparallel) + ("r-ff" ,r-ff) + ("r-ffbase" ,r-ffbase) + ("r-foreach" ,r-foreach) + ("r-genomicfiles" ,r-genomicfiles) + ("r-genomicranges" ,r-genomicranges) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/gQTLBase") + (synopsis "Infrastructure for eQTL, mQTL and similar studies") + (description + "The purpose of this package is to simplify the storage and interrogation +of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, +and more.") + (license license:artistic2.0))) + (define-public r-gqtlstats (package (name "r-gqtlstats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 76236929de..bc483e6f13 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10549,53 +10549,6 @@ views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.") (license license:artistic2.0))) -(define-public r-gqtlbase - (package - (name "r-gqtlbase") - (version "1.21.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "gQTLBase" version)) - (sha256 - (base32 - "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) - (properties `((upstream-name . "gQTLBase"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This is an upstream bug. - (add-after 'unpack 'fix-imports - (lambda _ - (substitute* "NAMESPACE" - ((".*maxffmode.*") "") - (("importFrom\\(ff,.*") "import(ff)\n")) - #t))))) - (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/gQTLBase") - (synopsis "Infrastructure for eQTL, mQTL and similar studies") - (description - "The purpose of this package is to simplify the storage and interrogation -of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, -and more.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 10/10] gnu: r-ggbio: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 23 Dec 2020 18:07:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 45399@debbugs.gnu.org Cc: zimoun Received: via spool by 45399-submit@debbugs.gnu.org id=B45399.160874681712622 (code B ref 45399); Wed, 23 Dec 2020 18:07:08 +0000 Received: (at 45399) by debbugs.gnu.org; 23 Dec 2020 18:06:57 +0000 Received: from localhost ([127.0.0.1]:54104 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XI-0003HQ-Nt for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:57 -0500 Received: from mail-wr1-f42.google.com ([209.85.221.42]:36056) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8XB-0003FF-KY for 45399@debbugs.gnu.org; Wed, 23 Dec 2020 13:06:50 -0500 Received: by mail-wr1-f42.google.com with SMTP id t16so73211wra.3 for <45399@debbugs.gnu.org>; Wed, 23 Dec 2020 10:06:49 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=yiPYQ4gH0qWC9Hizov0oQITO4DIkZSfqJFlBXahYh7M=; b=l4g9pnxpAPN5UU2Vrpapb41OJVFwyD6PGdcY2eColA8rrXKDWIoRwtGm6BB1uMPKQB aEKOTXfF2Qei8J7nJosHJ0+dSmibs7C5LgZDfnCTpm5FP1suJf6HtSbuhPZJLjQvYuxj bm/ZlOS/l1gQnb3IcwMOi6m4YCc0+kQMgnR3fSfVGy9t31vQIwMFeRgiWmAzq3yFCTye +07KJdlCVp/Hyy1ogjXlDgAKWQ2mLg1pAyg/1LwmPOIvQQ9ACq+CpRFAFRfRmTxv/dwR e/mT+AvRaL1WpkG+UK2sdBj3mrkpC0zDok/SB1dBuEOiwG1ta9LgFV/Mhi3bKHphAAkJ jgBw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=yiPYQ4gH0qWC9Hizov0oQITO4DIkZSfqJFlBXahYh7M=; b=MCOAea3IUaKo3djmThy9VxLoo3RgvNNqPouLFi8X563FhZnE/lpC2b0Hxnzgdcsmq1 HMN9lNFU5y9NhNZD/uuSY/is9zFSti44btLNsV9KF+LdlvVFNroaD1LIVB8NIUM1/oYf XwrWUiGmErpJ8I30fZcCCahZYiLQ/jI1N8NMnR/ydM+4x/lICbj6pcOf/rZRP9BfN5C+ 9oVWfKvXYucjP9cZh03ov8ODf13ZxzIoXumM+YAqXYmH2AoGCYkZDcHcbUxAfm9Kj3RC brwE6ZxlytPp6QBXg91m1yYPhJcVCG0sBz7p7+QbRYHzFE34ta/TIv5Pb4p8MxBYWxyE n1Ug== X-Gm-Message-State: AOAM531zv3BYfGJ1FUMru5WwUmNDRSJYxNcTexIaUjYpxI+HouC92c24 RBI5gvm3uE0XPADaiC0IClJ1As9rrgk= X-Google-Smtp-Source: ABdhPJztjMt4gk+zoj1LBYqB9njKO1Gj75FwqjplOv+Fi2Y2wWdHDWlpDqITBWWoPl8sixJWBeQRzQ== X-Received: by 2002:a05:6000:cc:: with SMTP id q12mr31161735wrx.335.1608746804215; Wed, 23 Dec 2020 10:06:44 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id a25sm583894wmb.25.2020.12.23.10.06.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:06:43 -0800 (PST) From: zimoun Date: Wed, 23 Dec 2020 19:06:35 +0100 Message-Id: <20201223180635.58647-11-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20201223180635.58647-1-zimon.toutoune@gmail.com> References: <20201223180635.58647-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) 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-ggbio): Move from here... * gnu/packages/bioconductor.scm (r-ggbio): ...to here. --- gnu/packages/bioconductor.scm | 65 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 65 --------------------------------- 2 files changed, 65 insertions(+), 65 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3dd93e763..55df9bf7d1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9308,6 +9308,71 @@ metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.") (license license:artistic2.0))) +(define-public r-ggbio + (package + (name "r-ggbio") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ggbio" version)) + (sha256 + (base32 + "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; See https://github.com/tengfei/ggbio/issues/117 + ;; This fix will be included in the next release. + (add-after 'unpack 'fix-typo + (lambda _ + (substitute* "R/GGbio-class.R" + (("fechable") "fetchable")) + #t))))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationfilter" ,r-annotationfilter) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-bsgenome" ,r-bsgenome) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggally" ,r-ggally) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-gtable" ,r-gtable) + ("r-hmisc" ,r-hmisc) + ("r-iranges" ,r-iranges) + ("r-organismdbi" ,r-organismdbi) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://www.tengfei.name/ggbio/") + (synopsis "Visualization tools for genomic data") + (description + "The ggbio package extends and specializes the grammar of graphics for +biological data. The graphics are designed to answer common scientific +questions, in particular those often asked of high throughput genomics data. +All core Bioconductor data structures are supported, where appropriate. The +package supports detailed views of particular genomic regions, as well as +genome-wide overviews. Supported overviews include ideograms and grand linear +views. High-level plots include sequence fragment length, edge-linked +interval to data view, mismatch pileup, and several splicing summaries.") + (license license:artistic2.0))) + (define-public r-gqtlbase (package (name "r-gqtlbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc483e6f13..512abcd8fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10484,71 +10484,6 @@ high-level packages for biological data visualization. This saves development effort and encourages consistency.") (license license:artistic2.0))) -(define-public r-ggbio - (package - (name "r-ggbio") - (version "1.38.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ggbio" version)) - (sha256 - (base32 - "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; See https://github.com/tengfei/ggbio/issues/117 - ;; This fix will be included in the next release. - (add-after 'unpack 'fix-typo - (lambda _ - (substitute* "R/GGbio-class.R" - (("fechable") "fetchable")) - #t))))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "http://www.tengfei.name/ggbio/") - (synopsis "Visualization tools for genomic data") - (description - "The ggbio package extends and specializes the grammar of graphics for -biological data. The graphics are designed to answer common scientific -questions, in particular those often asked of high throughput genomics data. -All core Bioconductor data structures are supported, where appropriate. The -package supports detailed views of particular genomic regions, as well as -genome-wide overviews. Supported overviews include ideograms and grand linear -views. High-level plots include sequence fragment length, edge-linked -interval to data view, mismatch pileup, and several splicing summaries.") - (license license:artistic2.0))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- 2.29.2 From unknown Tue Jun 17 01:50:41 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: zimoun Subject: bug#45399: closed (Re: [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor).) Message-ID: References: <87czyslg2f.fsf@elephly.net> <20201223180338.58588-1-zimon.toutoune@gmail.com> X-Gnu-PR-Message: they-closed 45399 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 45399@debbugs.gnu.org Date: Tue, 29 Dec 2020 16:43:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1609260182-5540-1" This is a multi-part message in MIME format... ------------=_1609260182-5540-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #45399: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioc= onductor). which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 45399@debbugs.gnu.org. --=20 45399: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D45399 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1609260182-5540-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 45399-done) by debbugs.gnu.org; 29 Dec 2020 16:42:31 +0000 Received: from localhost ([127.0.0.1]:40031 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kuI4t-0001Q9-1m for submit@debbugs.gnu.org; Tue, 29 Dec 2020 11:42:31 -0500 Received: from sender4-of-o55.zoho.com ([136.143.188.55]:21561) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kuI4p-0001Pt-Ka for 45399-done@debbugs.gnu.org; Tue, 29 Dec 2020 11:42:29 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1609260145; cv=none; d=zohomail.com; s=zohoarc; b=hM0tuwyOaecJZCusGJLLjs+TYQHy/U5pLqQy9hJ4Zk/6SB8OQ+O31Efq3R0giTKZBrvW9RCUvpL7SIGXqj3U1hUrJBHyKV8E3soVKajR8mopFqSNWMhY0MroaomvY7Ud8FLSPAPz1cAOSMO2YncxHJarWoZjc5BuCtZbK9AaPrs= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1609260145; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=069PcKwo/SVLqof+yBpB4qzBSxQ+Wf9D4ubnZs3213g=; b=k+gKM+sAZiu+iXB4Wfs3L4VbYKLwGlqPqPX/LJQL1u+kAjo8FkFv6L0PZXGQiH+B0JrdoGCI+GrUbmiqTdM4yh+id64q37LU+4nn3COk8Wsk6MGEapkTlAU2xBpoMGl+SYDdrX0LVUvv9OWxRCU+vi+eJUQO/tV+x74lLl3EF10= 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= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1609260145; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type; bh=069PcKwo/SVLqof+yBpB4qzBSxQ+Wf9D4ubnZs3213g=; b=JXdawaMrXAaU1B1CR/loYJPPYOR89gLpwZl3QyJGMxynutvbSMU1ZEpt6PghDaTc 1dd6NCNPjZrdjjEmsHXcgxZpITjjc13ZcLkRmtprhkmjLyvbVAeOcX5AGm/IUWE6dIO PksMm3QaEj0zuSuvx6RPcQQnF4mRNKp1/CSd7Pas= Received: from localhost (p54ad4f8d.dip0.t-ipconnect.de [84.173.79.141]) by mx.zohomail.com with SMTPS id 1609260140137930.6630903074996; Tue, 29 Dec 2020 08:42:20 -0800 (PST) References: <20201223180338.58588-1-zimon.toutoune@gmail.com> User-agent: mu4e 1.4.13; emacs 27.1 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). In-reply-to: <20201223180338.58588-1-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 Date: Tue, 29 Dec 2020 17:42:16 +0100 Message-ID: <87czyslg2f.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 45399-done Cc: 45399-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 (-) zimoun writes: > Hi, > > Janitor [1] patch set. It moves Bioconductor packages from (gnu packages > bioinformatics) to (gnu packages bioconductor). Far to be complete; still 7 > pacth set like this one are coming... > > 1: Excellent! Pushed with commit 610cd6a170. Thanks! -- Ricardo ------------=_1609260182-5540-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 23 Dec 2020 18:03:59 +0000 Received: from localhost ([127.0.0.1]:54057 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8UQ-0003A6-Vc for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:03:59 -0500 Received: from lists.gnu.org ([209.51.188.17]:34028) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ks8UO-00039x-CT for submit@debbugs.gnu.org; Wed, 23 Dec 2020 13:03:57 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56266) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ks8UO-0001Jb-7A for guix-patches@gnu.org; Wed, 23 Dec 2020 13:03:56 -0500 Received: from mail-wm1-x32a.google.com ([2a00:1450:4864:20::32a]:38725) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ks8UM-0000JT-JA for guix-patches@gnu.org; Wed, 23 Dec 2020 13:03:56 -0500 Received: by mail-wm1-x32a.google.com with SMTP id g185so190390wmf.3 for ; Wed, 23 Dec 2020 10:03:54 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=CSQWs/RwKhPbNk4OKKfU3SNdZr6jiTdKVhKpCQqE4VI=; b=uYeI8gNdAXY6zwxDq86YKSoSRmgs6ye93ccCnY+QcupTVnbAVhe2HQvDaV9uuJ379p CoVY+/KP42xxvV3G8BBy8iXcH4cQSFItZstcEHnX2QnexkQlL/GnXbuJ07oezosmgd0J gRb6ci4WvecVCcBQxwLIjRPd1Hu584rx/F0+kgRLWTSVCuOfTfUuaQlr0Jmie4mBCtwK APny4cTK8BzGMHXeEL5ZTn2zYZhaHo50CAWBKQAsXA8ze3WGlLGv/G6FoBxeYkrUk9sl jMg35xW7NzFSUa2/BwAwMHk99fqgrJObrfZI/fYC+h8mgzA/cdl/wifpDVcoCAa70xMv +YAQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=CSQWs/RwKhPbNk4OKKfU3SNdZr6jiTdKVhKpCQqE4VI=; b=sGsbmNuOqXmlBAd74mPDRBOzp3kIcaVDrnNJBFMqv8qBe+CN8zPf+nyLCxwc9UDMQ1 DA6uCAMr+Vj5vFjuN5S/+Kvi18Ab+w1LduCe8+GRKCySqx/LnAuZdj2uwLCb2CMO4sm3 2rKVYTMnZQFK9OQYkoFqPJ31iuOAjYZyr71yWGIRlaeIezQ84+QrpWxapBo1F7zqtD4M OsFuGRKQ2IaP7t8+Ul4toTpGNCSFaEmyJfaMkll+TjS5gft2heqf0Vm2EQWPyxyBzxFT zpRrJnLXGdZDeVthAblOt3//oU97+aoxq7zHC9IGOvwVIoQdq/eqD74aSUcV+GS8xvfq Z6gg== X-Gm-Message-State: AOAM530NGzz6JsR78jAA2lskguAUE2mW8MtAfrK2PrqiCbA550BhVsna AV2mxHRP/9d797yp3psKcg6GXmlCzjw= X-Google-Smtp-Source: ABdhPJw2kdFErSPo6O6UPHctWfA1FKhnLO8X0eKTfZ9o/ocwVWPGWwJXFz6gRIdEiaXKdDBif3t4Pw== X-Received: by 2002:a1c:b742:: with SMTP id h63mr820871wmf.122.1608746632923; Wed, 23 Dec 2020 10:03:52 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id h5sm37512466wrp.56.2020.12.23.10.03.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 23 Dec 2020 10:03:52 -0800 (PST) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Date: Wed, 23 Dec 2020 19:03:38 +0100 Message-Id: <20201223180338.58588-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::32a; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32a.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 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, Janitor [1] patch set. It moves Bioconductor packages from (gnu packages bioinformatics) to (gnu packages bioconductor). Far to be complete; still 7 pacth set like this one are coming... 1: To transfer the Copyright, I use: git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r- Then, after the move, I run: ./pre-inst-env guix build r- --no-grafts ./pre-inst-env guix build r- --no-grafts --check and at the end of the series, I run: make as-derivation to check that "guix pull" is not broken; just in case. Last, I have not carefully checked the imported modules, so it could be possible to perhaps remove couple of #:use-module (gnu packages ) in gnu/packages/bioinformatics.scm. All the best, simon zimoun (10): gnu: r-sushi: Move to (gnu packages bioconductor). gnu: r-gwascat: Move to (gnu packages bioconductor). gnu: r-gviz: Move to (gnu packages bioconductor). gnu: r-gqtlstats: Move to (gnu packages bioconductor). gnu: r-ldblock: Move to (gnu packages bioconductor). gnu: r-erma: Move to (gnu packages bioconductor). gnu: r-homo-sapiens: Move to (gnu packages bioconductor). gnu: r-snpstats: Move to (gnu packages bioconductor). gnu: r-gqtlstats: Move to (gnu packages bioconductor). gnu: r-ggbio: Move to (gnu packages bioconductor). gnu/packages/bioconductor.scm | 400 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 405 -------------------------------- 2 files changed, 400 insertions(+), 405 deletions(-) base-commit: 4994e1f2bd9b573d2c13abf2b98ec204f510ad11 -- 2.29.2 ------------=_1609260182-5540-1-- From unknown Tue Jun 17 01:50:41 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#45399] [PATCH 00/10] Move some Bioconductor packages to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Dec 2020 09:15:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 45399 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: 45399-done@debbugs.gnu.org Received: via spool by 45399-done@debbugs.gnu.org id=D45399.160931965730505 (code D ref 45399); Wed, 30 Dec 2020 09:15:02 +0000 Received: (at 45399-done) by debbugs.gnu.org; 30 Dec 2020 09:14:17 +0000 Received: from localhost ([127.0.0.1]:40885 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kuXYf-0007vx-3j for submit@debbugs.gnu.org; Wed, 30 Dec 2020 04:14:17 -0500 Received: from mail-wr1-f50.google.com ([209.85.221.50]:42324) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kuXYc-0007vj-Ox for 45399-done@debbugs.gnu.org; Wed, 30 Dec 2020 04:14:16 -0500 Received: by mail-wr1-f50.google.com with SMTP id m5so16841607wrx.9 for <45399-done@debbugs.gnu.org>; Wed, 30 Dec 2020 01:14:14 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:in-reply-to:references:date:message-id :mime-version; bh=eI5b/XxfGUwvZGjm2Ds/hV2mJa86bIpCt+KARfTM8sI=; b=ouKrw53Iu0B4aqqm3jobZ+Hqr3fKAPy9kWmu17a42spaNo16rkU5Yqcc9539C9WmUN FO2/52b6vNxzN7Y7uXnVyeLFugjLv3y9HDiKefOaHhci/uOhaupr0cL3v7R9dojPs/3v yaF84Z6p43CpadIeC1JUZI6YntchNpWRObo+iEd8O76C7mGZK85dAH5xqbwPY+fCDk9R X1VDVcUwEakxlbS4V/fhBw5zN9Uh0GyfhOxzwZKfpMNRb7NPAVoPntaeM+redXZirMbC scAN2Qjj9WKIxF3CWZa3TCeWePLc1HyrbhdfBgvLT4AWGlf8+NLH3bQ6Xs8jr84ymoil dE1Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:in-reply-to:references:date :message-id:mime-version; bh=eI5b/XxfGUwvZGjm2Ds/hV2mJa86bIpCt+KARfTM8sI=; b=hUZ5J8I1w24Tqg0piXDL1fQGIpqSww++7gsXhFsH8zMrQJ1BPzgpN7Ha5VirNUSIMv 0JctwBZ+JJecXhuMWiSGAX1Mihp0EQ4IWccV4RtpWilL+UcMO3LwmJMAT6tOS0uSrxRE 8mD8bKmrg43jvcB16myCuUpq8dRYYfqPWYazVBif5r2zVUZZJTI3b/rIYETj1JMI6He6 TcFUPeB8dGhbWqE5dP258jJzMiI7L3rYKooMmtbqE342iRPgrPinGmZngDJ96jCdn/XJ +UUTZ0z/dsKCAuVMsibPWvQt6uOLcQ8gTDCQzuxe5Cqv8xJPsgClzHiivFQPeCDoRr2G gSbA== X-Gm-Message-State: AOAM533MbDwC0rAQrtnhZuVb1PvYbvRDqk6kC9NSVrWYERrNX+4ypSd3 ehuJCIawLiFDnUb26DxtMqsUYOmfbUQ= X-Google-Smtp-Source: ABdhPJxGlWIC7O4eHJj0QQk7AsZH02OP4JPyMBzo1+nDI04zkX5j5QHO1emPh3u6qAmOJvSrYd8VQw== X-Received: by 2002:adf:fbc5:: with SMTP id d5mr58840429wrs.82.1609319648937; Wed, 30 Dec 2020 01:14:08 -0800 (PST) Received: from lili (57.246.195.77.rev.sfr.net. [77.195.246.57]) by smtp.gmail.com with ESMTPSA id m2sm6185416wml.34.2020.12.30.01.14.08 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Dec 2020 01:14:08 -0800 (PST) From: zimoun In-Reply-To: <87czyslg2f.fsf@elephly.net> References: <20201223180338.58588-1-zimon.toutoune@gmail.com> <87czyslg2f.fsf@elephly.net> Date: Wed, 30 Dec 2020 10:13:29 +0100 Message-ID: <86sg7nsll2.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) 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 (-) Hi Ricardo, On Tue, 29 Dec 2020 at 17:42, Ricardo Wurmus wrote: >> Janitor [1] patch set. It moves Bioconductor packages from (gnu packages >> bioinformatics) to (gnu packages bioconductor). Far to be complete; still 7 >> pacth set like this one are coming... >> >> 1: > > Excellent! > > Pushed with commit 610cd6a170. Thanks. Well, I should change my workflow since I have missed [2]. 2: Cheers, simon