From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 06:23:39 2019 Received: (at submit) by debbugs.gnu.org; 30 Oct 2019 10:23:39 +0000 Received: from localhost ([127.0.0.1]:49279 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPl8d-0005MO-FA for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:23:39 -0400 Received: from lists.gnu.org ([209.51.188.17]:42481) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPl8a-0005MF-3G for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:23:37 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:39643) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iPl8Y-0006NQ-QW for guix-patches@gnu.org; Wed, 30 Oct 2019 06:23:35 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iPl8X-0008Va-Kp for guix-patches@gnu.org; Wed, 30 Oct 2019 06:23:34 -0400 Received: from mail-wr1-x42c.google.com ([2a00:1450:4864:20::42c]:37426) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iPl8X-0008Th-D5 for guix-patches@gnu.org; Wed, 30 Oct 2019 06:23:33 -0400 Received: by mail-wr1-x42c.google.com with SMTP id e11so1641651wrv.4 for ; Wed, 30 Oct 2019 03:23:33 -0700 (PDT) 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=orA0ET7lydW6D/3khvlaT/boglHrANY/BtO9Wq8JCsQ=; b=kweonFK/GTTm2aPosW4FKVZtgxi6TNvincHkQlVBfXBPogcYtyHhOGG59qEgOLfI2B 61f08Nrx0yy/02YGW1hRwkQHCZ6h1TVLfCIymLxBaLu+tuBE5lx9VPkdLgkJjpFT/IrR 5ZzWZo0gjcnLQ6HQORtE8bFGx26HgOu2lBIUv+JOD7BcddTLeiIiGsmE9cj4dRfkKf4f FEPetqGrUGcY3Se+a+SqLvFseGP/kRjIUTsmbabPWNG+WJcxDzY1BdMKrA3hNqk2kG2F agYmOYSPVWcUGEEQF1hRnG4WSexBSZvpb+Imk2LiKkUi5/VxrDdhMDcpcPJCvQ+HG6rv dqjQ== 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=orA0ET7lydW6D/3khvlaT/boglHrANY/BtO9Wq8JCsQ=; b=LxF0Kc80A0EKCZK16q3GXSXIgI2ZA/g49Btqyy5OJ1vmERmP2eHac8RTkM8hCAPoxy 6wfVWYgWydRrKAK/xVS9H6nPwVi4Lt14QJ+JwRY74VwLWsCN/6g0SZUqXdW78hzCrMQs e4md2667mk9eoDOe9N3EUoBRUfeYdk+SQYDifZQ2JNjziqfWNOA0GjQtc7W9Luu9fO0w 7D6yymMnMdicv3tsZr2QGLsHcO5aAybT3iMTqFF98Yfb8EjazdAAfuYXu4/539QHitH+ v7ZgtRMhldCrl1kaHmkTbqXVsJ7L9bHwI5l9Ct1x8W1gDkg2Nf6NZbmI7aZ+eaUBL+qn ouWQ== X-Gm-Message-State: APjAAAVeNmJKto5PUu7+VCLVV56D6xYrbsmdg/ZyKt4quFw/pOolrqbq UYbllVDHuX+NVOeLS7tjEiC5GibJ X-Google-Smtp-Source: APXvYqyPk8Fq6dYYEwwhVkkPRJJcSWHN9C5IGCJZ6u1WFCXs8sFzc6F0iYCwzM4wCimxxPYtkOG4lg== X-Received: by 2002:a05:6000:351:: with SMTP id e17mr22661813wre.96.1572431010331; Wed, 30 Oct 2019 03:23:30 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id 65sm3036181wrs.9.2019.10.30.03.23.29 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:23:29 -0700 (PDT) From: zimoun To: guix-patches@gnu.org Subject: [PATCH 0/6] Add flowWorkspace from BioConductor Date: Wed, 30 Oct 2019 11:23:24 +0100 Message-Id: <20191030102324.12437-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:4864:20::42c X-Spam-Score: 0.7 (/) 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 (--) Dear, The aim of this serie is to add the package flowWorkspace. It is important to notice that the package RProtobuflib [1] from BioConductor is not packaged using the correct convention. RProtobuflib includes its dependency protobuf-2.6.0 as an archive tgz and compiles it using its ./configure [2]. Therefore, the file ./configure from the unarchived protobuf-2.6.0 needs to be patched to apply the correct shebang. It is clearly unconventional and we should distribute our own version of RProtobuflib using the correct way i.e., packaging protobuf-2.6.0. However, do we want to diverge to the official BioConductor and add maintenance burden when we are not fully able to already package all the BioConductor archive? All the best, simon [1] https://bioconductor.org/packages/release/bioc/html/RProtoBufLib.html [2] https://github.com/RGLab/RProtoBufLib/blob/trunk/configure#L2860-L2889 zimoun (6): gnu: Add r-idpmisc. gnu: Add r-flowviz. gnu: Add r-rprotobuflib. gnu: Add r-cytolib. gnu: Add r-ncdfflow. gnu: Add r-flowworkspace. gnu/packages/bioconductor.scm | 173 ++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 30 ++++++ 2 files changed, 203 insertions(+) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 06:25:53 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:25:54 +0000 Received: from localhost ([127.0.0.1]:49286 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAh-0005UI-88 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: from mail-wr1-f50.google.com ([209.85.221.50]:34625) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAc-0005Tv-HK for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:45 -0400 Received: by mail-wr1-f50.google.com with SMTP id t16so1664710wrr.1 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:42 -0700 (PDT) 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=9cMYqmaR/LIMgB3R2l2Dtxwtg+DR5wGOW5GznpttjNY=; b=seyLk6zlVOxAp07Xq7nMTncOW0ex+JUR+NM6slM2Op5UNLFmqquc2fRFZeeYDC+A0u Ceg/Q7PKKYHkZnLViyZm7B9N2X6bxollEZ+al5DmQljjYD/Nc2qOixEfX6FPIIPUKXRI 7dXYFGoXe7S7+mHkx0nNVljY2Q61FmNL/ASuttJ42QuyN97V3m6bSNnxE2x/N0YI9ofv pLNSLn3EXvPveco3bRiX9hHZJTHCwsVWqsFXE9b0DZwW3FZsjCfsQbYyrKgjOp0qxjP1 OTeK4b32fkzAuywpzzJ5xhUwvnzbPSE3zCn+zz6+sWpbkV/YNxRhd6M5cpm17opXCn2e 8Pow== 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=9cMYqmaR/LIMgB3R2l2Dtxwtg+DR5wGOW5GznpttjNY=; b=cu4pjXgVQFizBJ2R94jR79UA+CAxYuOaxt3qdVWa2CaC7Saq6rbh35Cg52F1jfNIU+ AL47b3ORt8ajkdVH+Yxfg7fgnAIv/Wk8y/5O4/d4QUXVHqN9EnX+M/F4/1mO65LtJitf jkUeCZN4i23gy/ycJ86ArSBjp6Tu+KwI/dZ7UnQUhy+ks8y7F/rfdPLJ5H+b9ek+qiWc J+nQJ8ushWRFyA3oD5lO+chlScDLzcbUfCRkfVVkH+uayuRkwxV+NHTnLrREJOnRZtJh tl/tIMAmzvkemnp55FHjEsFcf9YBV3QIuZknCFIkujx1MebgJhbxeHhHv0k9RiOXFl3R jptg== X-Gm-Message-State: APjAAAV4xJb58RBgsf16iJKypxp8KE0IycN5HUDvaEhRuwL53p8G4lPW pNYm91ZZzTPLUsLgUHzkvY0h2pFx X-Google-Smtp-Source: APXvYqx58Tx5JTTDExA/re1AIxH/nU1bqLgHAeX1k9TI6vB8v3XIpNw16LI2/LUrlN5vDY4Kt2mQaA== X-Received: by 2002:adf:c409:: with SMTP id v9mr23955652wrf.41.1572431136409; Wed, 30 Oct 2019 03:25:36 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.35 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:35 -0700 (PDT) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH 1/6] gnu: Add r-idpmisc. Date: Wed, 30 Oct 2019 11:25:26 +0100 Message-Id: <20191030102531.12495-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/cran.scm (r-idpmisc): New variable. --- gnu/packages/cran.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b16b96dc77..f47eafc3bb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2018, 2019 Brett Gilio ;;; Copyright © 2019 Nicolò Balzarotti ;;; Copyright © 2019 Wiktor Żelazny +;;; Copyright © 2019 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -15653,3 +15654,32 @@ unique identifiers, and whether it is a certain length. In addition, files and to efficiently import multiple tabular data files into one data.table.") (license license:gpl3))) + +(define-public r-idpmisc + (package + (name "r-idpmisc") + (version "1.1.19") + (source + (origin + (method url-fetch) + (uri (cran-uri "IDPmisc" version)) + (sha256 + (base32 + "13qcvfm703frs367paddz1wq9k3p17f9p5347m56bhky5hjkaphd")))) + (properties + `((upstream-name . "IDPmisc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "https://cran.r-project.org/web/packages/IDPmisc") + (synopsis "Miscellaneous tools of Institute of Data Analyses and Process Design") + (description "This package provides different high-level graphics +functions for displaying large datasets and circular data in a very flexible +way, finding local maxima, brewing color ramps, drawing nice arrows, zooming +2D-plots, creating figures with differently colored margin and plot region. +In addition, the package contains auxiliary functions for data manipulation +like omitting observations with irregular values or selecting data by logical +vectors, which include NAs. Other functions are especially useful in +spectroscopy and analyses of environmental data: robust baseline fitting, +finding peaks in spectra, converting humidity measures.") + (license license:gpl3+))) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 06:26:00 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:00 +0000 Received: from localhost ([127.0.0.1]:49292 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAp-0005V0-T7 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:56 -0400 Received: from mail-wm1-f65.google.com ([209.85.128.65]:52830) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAg-0005U2-Or for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:47 -0400 Received: by mail-wm1-f65.google.com with SMTP id p21so1491399wmg.2 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:46 -0700 (PDT) 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=nUws7C2qD+TDFt4SyqllH9cDNq7wx4R1DjuW4Rh2tFA=; b=u5k+aelhh9+Q6ZA5qOSdTIPNuRFG4RU3xAQ/e3HuBNKSaXFwlyZD7AFpzFhukkm2/O lSbx/0i9bcBZdgYeTF9WUoOz/MYvJOzCoHpXos7j4cTZjSWZBJPkREhLH5pmUxGXPNgj L8rVh9xi7bx3raCn+ywp348RafqWMXR/47NNG18BQTnQ2WLD2ZqIwMsyJ1Cauib7GLi4 wdrRyK3WhPX/RWFE64xj/sr2WJaySQcsple1uQutjJvFBg3xA23nhq20j/0lHmcLjoUE GTODQ4mGtNbYz4QlspuHKSi3MGjgbJztm5ZGApg2Uie9wZnbuzQD7p+HGpXhX0xaDfNW VqXw== 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=nUws7C2qD+TDFt4SyqllH9cDNq7wx4R1DjuW4Rh2tFA=; b=Mo3h/Q/RnpZPYMQRmIHnXMTV1p31JlO7cqdLweVHR8pKpPyvj5/hJc60RlPDWet85J J07WNU9AxPf57g8g+9d7JQppreMOdUnLYAPzraBs9OOME+LObcWgWvuNta0rcmnErLQH CE205fVXzhTEQZd6k1VTFufqU4MU1ehVfwAqOWjxfgKsDgSjOnm4Ru/NKZaGhJ9k7pTk rJpqa+AlX920891pK2R7YwhnnybQfTVO62BbCM8UxEXvwh4JUsovBdp3YTEov7IScyWL m4p+ZSwasYkd1I8REAIyhqxQXPzHj1Bf/yYd2eR+vzgerPf1txOJYarEn4LLsU2hK7c1 5/7g== X-Gm-Message-State: APjAAAU9hMBCgejnYWGQLTBmsgcF0XKMGdEqosDU6b3qAVmno0ajlOZg bmj5r7/IfcYXZ0aczkt9xsIwh/nc X-Google-Smtp-Source: APXvYqyaBbTmW0uzF2eqLBSVCoIeTEcfR14FsRPSiiF1H1GSnSE2mzeWEB9mhCL8sEkFuBZIYleoHA== X-Received: by 2002:a7b:c76d:: with SMTP id x13mr8375901wmk.155.1572431140703; Wed, 30 Oct 2019 03:25:40 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:40 -0700 (PDT) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH 2/6] gnu: Add r-flowviz. Date: Wed, 30 Oct 2019 11:25:27 +0100 Message-Id: <20191030102531.12495-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-flowviz): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6467fecb8c..92e5d3ec0b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6137,3 +6137,32 @@ features (e.g. genes, microRNAs).") data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) + +(define-public r-flowviz + (package + (name "r-flowviz") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowViz" version)) + (sha256 + (base32 + "00zwfzpdln62160h1ahcki5b96y06a1na7xjqs63b7571318xj20")))) + (properties + `((upstream-name . "flowViz"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-flowcore" ,r-flowcore) + ("r-hexbin" ,r-hexbin) + ("r-idpmisc" ,r-idpmisc) + ("r-kernsmooth" ,r-kernsmooth) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://bioconductor.org/packages/flowViz") + (synopsis "Visualization for flow cytometry data") + (description "This package provides visualization tools for flow cytometry data.") + (license license:artistic2.0))) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 06:26:00 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:00 +0000 Received: from localhost ([127.0.0.1]:49294 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAu-0005V6-51 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:00 -0400 Received: from mail-wr1-f68.google.com ([209.85.221.68]:41219) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAj-0005UA-HR for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: by mail-wr1-f68.google.com with SMTP id p4so1633895wrm.8 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:49 -0700 (PDT) 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=M0rGms2nvbWS20tLFPIynEvDoGLaGhMxz3isshnakiA=; b=gjsSQyQjI7tclSqkDplypyrzcLqNY4GN2mtG+vDjZyuOZURF6LlFOP3FAeWoJdvqnt 60POUtQk7Vz/2Bkxo1jMxwHAEHGI7LFcaDXK3mMH2CNG3YgeCTEsJP8CDQ34fGOaCyYL gDCjxo4gLC4jtiSGHcN8BsCuJo9xhtsv9Ei9Io0F2SCL/ibwMFCzpE2kj/Uu1PPLG6U0 y5Mmv2c1xdJCUzclQUKjOl+HEPhF8BE1L5Rf12LfLkFXRrBNERhPzZdPHFH9vI0MJEH8 lEyFUJpEiwRIbqGkQ9DfW4n21Ocs3cf5+kNJiwGh8/nIpNkCpyuDAonT0CNg36avgPGO FU0Q== 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=M0rGms2nvbWS20tLFPIynEvDoGLaGhMxz3isshnakiA=; b=aB+zPXwe5IootGzGUsHh3NO92HXSfIkx7cYE4QY6NS51nSMaTrzgbm53Sf7xBepXeS mCyQ5EwiHPIheXc0Qi1tjWH8OWOrhLXN0mW5/Ig+tVYoNib3Kioh8h90yEZ4JOEXY5Lm z85Lur4JTQfRy+1uKa3VBfA/WPli9lqDZPMYJ9aA5Iv5FNuP2aMZZp2w68X9OvshrafB AY7ddId9ANEovgiEZTZTCXsHjbKjYyQVao4OPqFmQXqGzzH3AaYmYe4qKmqEqWf6Xzss 41B0jBpFqoEHGXf2l1gTjqH2G/d5xI9cPr5G3Z725KdNgMFRQF3GLenwBSu08Sznh16n qsIw== X-Gm-Message-State: APjAAAUU487F1tuHITxjB2yG8fJrmspq82bJUZP84sojXRQn/pyy10Mz KXBXSA+Lmu5lOj3z8NzAGeGJCFkK X-Google-Smtp-Source: APXvYqzEXQzBD6ORavqs/MGBtKWXqG/+HjoSEt61N12QO3Iz9yTqdn16lfEbsBX0VNcXrA5XOe2OmA== X-Received: by 2002:adf:f547:: with SMTP id j7mr5580227wrp.69.1572431143799; Wed, 30 Oct 2019 03:25:43 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:43 -0700 (PDT) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH 6/6] gnu: Add r-flowworkspace. Date: Wed, 30 Oct 2019 11:25:31 +0100 Message-Id: <20191030102531.12495-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-flowworkspace): New variable. --- gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2636095e0f..dabfcb2cb3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6260,3 +6260,53 @@ represent and interact with the gated cytometry data.") "This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.") (license license:artistic2.0))) + +(define-public r-flowworkspace + (package + (name "r-flowworkspace") + (version "3.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowWorkspace" version)) + (sha256 + (base32 + "1r1xxqzlp2x2gf79f37ckninnyjkxcb7xz7rffg2nadmapl5shvw")))) + (properties + `((upstream-name . "flowWorkspace"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-cytolib" ,r-cytolib) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-graph" ,r-graph) + ("r-gridextra" ,r-gridextra) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-matrixstats" ,r-matrixstats) + ("r-ncdfflow" ,r-ncdfflow) + ("r-rbgl" ,r-rbgl) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rprotobuflib" ,r-rprotobuflib) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page + "https://bioconductor.org/packages/flowWorkspace") + (synopsis "Infrastructure for representing and interacting with cytometry data sets") + (description + "This package provides importer for basic workspaces from the proprietary +software FlowJo into the BioConductor package flowCore. It is designed to +facilitate comparison of automated gating methods against manual gating. +Gating hierarchies, groups of samples, compensation, and transformation are +performed so that the output matches the analysis from the proprietary +software FlowJo.") + (license license:artistic2.0))) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 06:26:01 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:01 +0000 Received: from localhost ([127.0.0.1]:49296 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAu-0005VD-NS for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:01 -0400 Received: from mail-wr1-f68.google.com ([209.85.221.68]:39867) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAh-0005U4-9D for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: by mail-wr1-f68.google.com with SMTP id a11so1643415wra.6 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:47 -0700 (PDT) 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=IRQX+ltzgQQQCLJNrNgluNhY+yKeEN3wmYeHe2/L9Gc=; b=X4axORuWVXmRxnoXVcQdoZcvwOMLOS52xSOlBC0PH48QmPWP7Nnjx7myhw814kGOCq s/IgG1Rk8FJGIS4s+JWPOk09M3wD/5mCOZnbcs2yQdJngq+UR+wy8LtyFMxU9p28JG/U PR+iRIRfR46XFhnmJhm7h0bi/TxEIIMsareyDODoeK87bU/cbGth44NT2TJOy9DkAqPb T9BI0upSC391cC9zC8/F6YFiedrTKH/nFO7PKeud/2IGBjcfQpa98KVKFjXBBmBRyWcK Gg7Yzvg3/TdnFz0ohvnohawdo8KwMAV2vif6CL2YLdQInYOOjkufKTlTFMzSpHMivCC7 uWQA== 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=IRQX+ltzgQQQCLJNrNgluNhY+yKeEN3wmYeHe2/L9Gc=; b=Z2UFmiNU0x0DFLFij3lkR1ekZZLpwi9TT9RC31MQs6wRNzG+a8xWCLWI4O2jPCUcGR M1HNBDbKDV3iVge+qY+ded856J/x8pGsWfZ/RHv6amf4+otJO+nK0piW3VdnE3cTYWcN tY9L/QxIXQj0AYlCGJjikd535YR+Zp2BHtx+0jZFpGoAVMK2uD2bZRXfkrqr3733nB+7 AGhYgqS46B+Z4KMHoCEo4hUv3zLHb0wcePVji+xDt2RkN5bP3FT4Z+FWdzSCLqj8kRvn 55/PKzOu4O5nDkaKIdLkrveZwF/UfQgh4GC+mcp3Fe+cRpMcaSfyBhKx5gYuRUvI85R/ QYOQ== X-Gm-Message-State: APjAAAV86jMSuUdnwvaM+uEQP6HdiLz+pdRgPvXIAROJJHbb0BCf56XS znrUkHf9QGFy2EEJiw66ZW9X+2h+ X-Google-Smtp-Source: APXvYqyduEC57JABGmz9n6Z9134SIPlSSPsymLWu9z6tf7leY7U/gmyCsIfBvWUFUs8S7tlqOdtQvA== X-Received: by 2002:a5d:49c9:: with SMTP id t9mr24899332wrs.146.1572431141271; Wed, 30 Oct 2019 03:25:41 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:40 -0700 (PDT) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH 3/6] gnu: Add r-rprotobuflib. Date: Wed, 30 Oct 2019 11:25:28 +0100 Message-Id: <20191030102531.12495-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable. --- gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92e5d3ec0b..7c1761852c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6166,3 +6166,42 @@ data.") (synopsis "Visualization for flow cytometry data") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) + +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg")))) + (properties + `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Contains unverified binaries: + ;; src/win/lib/{i386,x64}/libprotobuf.a + (add-after 'unpack 'remove-win-folder + (lambda _ + (delete-file-recursively "src/win") + #t)) + ;; Fix non-conventional packaging. + ;; The dependency to protobuf-2.6.0 is included as tgz and build + ;; by the R package itself. + (add-after 'unpack 'fix-wrong-hard-coded + (lambda _ + (with-directory-excursion "src" + (invoke "tar" "xf" "protobuf-2.6.0.tgz")) + (substitute* "src/protobuf-2.6.0/configure" + (("#! /bin/sh") (string-append "#!" (which "sh")))) + #t))))) + (home-page "https://bioconductor.org/packages/RProtoBufLib") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description "This package provides the headers and static library of +Protocol buffers 2.6.0 for other R packages to compile and link against.") + (license license:bsd-3))) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 06:26:01 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:01 +0000 Received: from localhost ([127.0.0.1]:49298 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAv-0005VL-54 for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:01 -0400 Received: from mail-wm1-f67.google.com ([209.85.128.67]:54928) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAi-0005U5-4e for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:52 -0400 Received: by mail-wm1-f67.google.com with SMTP id g7so1483210wmk.4 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:48 -0700 (PDT) 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=FcZxrj0YZSeBRnqLcu/Ekvd3AWYSVWoCWNlHFphsfPs=; b=UvyrAbdwOYJWLwZMpq9nUhwAgit/UIsWJrNcO+QXXaESP5DBLVEakYYSZNCt10DYaW p049WElBzP2raCtk9ztl/Lm9zaf/LwTvOrI8g8YF9fgr5cezih4B9gw9udx5xneXd8V7 2VAw/YXw4tjh/63aF3KToEsbrufkNWBC71g3fvenC/xsVD8rWaEc4lRBYgtUHTDDl9+k 92gNA6JpnOFQfeCaiTVGN1FP6S/45M53WAsybZlKI3Ed1iA6pEWAzUf0rk7rkrjUS08o IUebQQJtw03V7xV+4tJjCDK6qv3zUXZhUgPzw3QxfCN4qtQ22MPTClgVcP5mqDdi6qBw xGhQ== 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=FcZxrj0YZSeBRnqLcu/Ekvd3AWYSVWoCWNlHFphsfPs=; b=AbQvN8MyzQB19Aw62SnifCOYzv19I7MnLeDGk37hfbf2ikNhqnQqLBRn+3k7bN25+N Nx4oVOEXjoZ9o/cV8oE+rg/FXN2bWIEsB51dnyodx3nDYv1MCuzT1LgoS4LggwWqcddw mgx1U0owqCFRCtIlMb3+v/hIWyZ3SZwLMi+B5hmUc3yFJjHF6lUkiP5skC+ccpmCjgQW hGp44PXTGfIkYAbhjRtdQzBPVwd7chIv1TTnr2rsovrNErY1eCGVXOoDJMTwem0dZte1 3mjaB0MRGkbti/Ymy8+PdxVDazkMfN3kt/ZhtNDGhJgAqdDCBYa0sgz2U78bxSi6kksJ qeEw== X-Gm-Message-State: APjAAAV/vN8FLnHwxBr5DJ8by9PXPARAoDBj3mZ412BSgQES1YEc7Qvc tLhQtZI7fH8fXKzp3cWhtFejPDp0 X-Google-Smtp-Source: APXvYqziPLoI9aw3UaSRs1kZqK6Xx7xP9wXTuK6/9RY2UhsCZOaKnwAv4kDErSb9I4lQqCnnP3dkjg== X-Received: by 2002:a1c:6308:: with SMTP id x8mr8402811wmb.140.1572431142301; Wed, 30 Oct 2019 03:25:42 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.41 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:41 -0700 (PDT) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH 4/6] gnu: Add r-cytolib. Date: Wed, 30 Oct 2019 11:25:29 +0100 Message-Id: <20191030102531.12495-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-cytolib): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c1761852c..a5c6e1ed55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6205,3 +6205,26 @@ data.") (description "This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.") (license license:bsd-3))) + +(define-public r-cytolib + (package + (name "r-cytolib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cytolib" version)) + (sha256 + (base32 + "10sdkwrmzmp3sh59hl3x0zxwlw77v80jnv8gz1qrv66skjb764cq")))) + (properties + `((upstream-name . "cytolib"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rprotobuflib" ,r-rprotobuflib))) + (home-page "https://bioconductor.org/packages/cytolib") + (synopsis "C++ infrastructure for representing and interacting with the gated cytometry") + (description "This package provides the core data structure and API to +represent and interact with the gated cytometry data.") + (license license:artistic2.0))) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 06:26:02 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 10:26:02 +0000 Received: from localhost ([127.0.0.1]:49300 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAv-0005VV-LH for submit@debbugs.gnu.org; Wed, 30 Oct 2019 06:26:02 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:46939) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPlAi-0005U8-Ts for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 06:25:54 -0400 Received: by mail-wr1-f42.google.com with SMTP id n15so1609993wrw.13 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 03:25:48 -0700 (PDT) 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=dr8HRKHlY7FqNgdC6GQexNyqk3uJt7l1BMmThsXxqlc=; b=gx+79W23Hvlzz1jBBHwaKZ3CyyPmP1v8AIEVIszOTIBst6tOIj512VbKF9tJwx59Hl YDyh3P6NeZZW9+rMziFKP8cZ5Q+PaEE5gJipUsEd9Lks/rFv132DjpUY44ORd9uelKso JvTZW1KZMsW6/e5FDJWbG1TJZs2gOG/t1w6uPFziWnzqWbfPUfrelyRARkeUZY7kJN79 QrmfYrmr1zT320Lm9f4doDpwPcze20WyEHHszXtIalmja5ZBaITHCRE2pyP6YZJop0Nq QmCjSD7uckRtHKex5O3HFNZuB+coyMVkFFrkzFqcXzFleD9n/DIJGrxxkRgBQc/EMxle iQyg== 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=dr8HRKHlY7FqNgdC6GQexNyqk3uJt7l1BMmThsXxqlc=; b=ieTL2jXGcxVx65D5DkyooQBOiu6X7+ZjJvfmwM/7QE86CfCsY2kU2ZWLYAQ2GdTly3 sxr/zyb8SvqDPgVnN99rMt2r36tgmY/MIOYR4jG8NTz5kyz4/e7kw+qb06gHaDLV5VKY 7F2vk1XbtrdnQDx/WO2B2pRjChrrlqFWkCl+U11qufSYJvci+lYrH9Y8BKY4JTyVh7f4 Nj1y5G3MQsXvL3j6LfFxlVPZvsDSvwS2yVCBJpZZseIVaVixZdqkiO3TO+N89dL8fZP2 Ygcl4QMEES6Xa7o6ZFwm1LB7ivfJ6UC7rI8/jMOQebW0h/MLmECB1Q1OFIziSB7xYs8b 6Yng== X-Gm-Message-State: APjAAAUSeRoi3OKcqIeHP/NQ7rpZlFHM5OHcVEjI2bgrqntMlXVIXq07 lwRcqkJVcs96y1c7vuj+gz67ZmHa X-Google-Smtp-Source: APXvYqxWNsEUqW273PK/4PpTjoLPBmP9ZxpjwM7tuITdJsmGIqZtXxBxx7RQuZS/0xd1adiDIZjD4Q== X-Received: by 2002:a5d:6b81:: with SMTP id n1mr23978369wrx.254.1572431143121; Wed, 30 Oct 2019 03:25:43 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id x205sm2493321wmb.5.2019.10.30.03.25.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 03:25:42 -0700 (PDT) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH 5/6] gnu: Add r-ncdfflow. Date: Wed, 30 Oct 2019 11:25:30 +0100 Message-Id: <20191030102531.12495-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <20191030102531.12495-1-zimon.toutoune@gmail.com> References: <20191030102531.12495-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-ncdfflow): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a5c6e1ed55..2636095e0f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6228,3 +6228,35 @@ Protocol buffers 2.6.0 for other R packages to compile and link against.") (description "This package provides the core data structure and API to represent and interact with the gated cytometry data.") (license license:artistic2.0))) + +(define-public r-ncdfflow + (package + (name "r-ncdfflow") + (version "2.30.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ncdfFlow" version)) + (sha256 + (base32 + "02769pr4gipjdlknhk8adica7v37c9fviffv0qscrf9v5j26rxzw")))) + (properties + `((upstream-name . "ncdfFlow"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-flowcore" ,r-flowcore) + ("r-flowviz" ,r-flowviz) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ncdfFlow") + (synopsis "Storage based on HDF5 for flow cytometry data") + (description + "This package provides HDF5 storage based methods and functions for +manipulation of flow cytometry data.") + (license license:artistic2.0))) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 07:39:21 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 11:39:21 +0000 Received: from localhost ([127.0.0.1]:49376 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPmJt-0002ts-Ev for submit@debbugs.gnu.org; Wed, 30 Oct 2019 07:39:21 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21184) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPmJr-0002tk-TC for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 07:39:20 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1572435557; cv=none; d=zohomail.com; s=zohoarc; b=IIdB4VLcKnvahahSQm4ZiZDVpqV05iPqKwBBqGjFBd0a9CgUFddhZrwMhPTrnDb/eZamQQuUIewY0Gjy2Pa6nwDgi74avMEiuqLS0LfVfFHA7QFdVm/Q9dgiEzAeZIEA4UQZ5NojVnNB6AvFmq6kP0KeBhznWXjkX8bHwNMR2sE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1572435557; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Nx7Cr3p/U5pCQ07ChqodIl7sTtrp+J6oM6k3AVdEjds=; b=FUxkNmwfVaV2PDi1lBRwh2Pv8mQOmg2EuKECNWQANzinitkYkOpZl1+uTUzZdpXCPEHaC5tLHx2bFgfgwiFed6Tu8pl+6EO/uXNwWto6ZiMl/5WE7wAq3JCBWsbTT8rKpGX9f2AqOkeXUjTWrl2cnJGNoWckib5ml63v12p/fvE= 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=1572435557; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:Message-ID:In-reply-to:Date:MIME-Version:Content-Type; l=1135; bh=Nx7Cr3p/U5pCQ07ChqodIl7sTtrp+J6oM6k3AVdEjds=; b=TLQ1Ise3i6taINLkk5YaqcLDWO7aJjMv5YJAGKINTZF66fhAY6bDc3aADpd8FCU+ c81+q9x1DuPOeqSGs9/s93Mx8bereNUQ/nH7wSqq4QfK/2rZtWRW0EJPG69dBXYl89V rH3a++F4NYsSyCDnRfVvBlthwCpeETIGoPIxMDAQ= Received: from localhost (p54AD4E25.dip0.t-ipconnect.de [84.173.78.37]) by mx.zohomail.com with SMTPS id 1572435555911171.5050938973559; Wed, 30 Oct 2019 04:39:15 -0700 (PDT) References: <20191030102531.12495-1-zimon.toutoune@gmail.com> <20191030102531.12495-3-zimon.toutoune@gmail.com> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib. Message-ID: <8736fah38i.fsf@elephly.net> In-reply-to: <20191030102531.12495-3-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: Wed, 30 Oct 2019 12:39:12 +0100 MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: 37988@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 (-) Hi, thank you for the patches! > * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable. > + (arguments > + `(#:phases > + (modify-phases %standard-phases > + ;; Contains unverified binaries: > + ;; src/win/lib/{i386,x64}/libprotobuf.a > + (add-after 'unpack 'remove-win-folder > + (lambda _ > + (delete-file-recursively "src/win") > + #t)) This should be done in a snippet instead. > + ;; Fix non-conventional packaging. > + ;; The dependency to protobuf-2.6.0 is included as tgz and build > + ;; by the R package itself. > + (add-after 'unpack 'fix-wrong-hard-coded > + (lambda _ > + (with-directory-excursion "src" > + (invoke "tar" "xf" "protobuf-2.6.0.tgz")) > + (substitute* "src/protobuf-2.6.0/configure" > + (("#! /bin/sh") (string-append "#!" (which "sh")))) > + #t))))) Can we just use our protobuf package instead of using the bundled sources? > + (description "This package provides the headers and static library of > +Protocol buffers 2.6.0 for other R packages to compile and link > against.") I would prefer not to mention the specific version here. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 07:41:38 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 11:41:38 +0000 Received: from localhost ([127.0.0.1]:49381 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPmM5-0002xN-SK for submit@debbugs.gnu.org; Wed, 30 Oct 2019 07:41:38 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21119) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPmM3-0002xF-Tb for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 07:41:36 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1572435694; cv=none; d=zohomail.com; s=zohoarc; b=CnTPcG3ZR5XM1svvq//A4hARDObiDkJ+0G2i8XPcuvLwahEb3Y7I/FUwlyseRDuoRjmnaXd6w/EeovoobR0jAbe4ggrzD8H+S+0ZRBRUfPlKS62dC3kIOm5X7BG+Q9TxcExjU9cBzI/skkCrOsB4zG2RyegSVs+w3IzBGi4IxPY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1572435694; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=yYo/Ybs9EFTCNEE9NzlszGv3/24WmxkxWmnsu4ZWRqA=; b=ftQiI9wd5r6L5hGP8XYVrnhSrZxQYb4p8igGXLBJiiS8mF2LNRt71q4X4MKyzVwvnA9PheJNpWLRk6xKWcwRgPra79/8Z4yftK9GlVFodhfCI7VlO8CZfE3weu12dD3ZCKGU0BYQMmmJUhtgGDgV/3ETN6tWXQMlO5QYsJcT4t4= 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=1572435694; 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:Content-Transfer-Encoding; l=604; bh=yYo/Ybs9EFTCNEE9NzlszGv3/24WmxkxWmnsu4ZWRqA=; b=M1rXZOyi5xmBiOVQmjeygiYtMCyZlJ0xGpndYbdJJ9StyYiomc6NChdmQP0kz24t 4xyln/1ZKeQuxbyJ0NuITdf1QYRCVx4N7C5BWgMMFL+3imb1zPX+g7eU92cB80qpAdS FbWBJwfHnbgs7/vIsPG1Pu7izbgK2XCWYVMc6eJ0= Received: from localhost (p54AD4E25.dip0.t-ipconnect.de [84.173.78.37]) by mx.zohomail.com with SMTPS id 1572435692229942.3306112462228; Wed, 30 Oct 2019 04:41:32 -0700 (PDT) References: <20191030102531.12495-1-zimon.toutoune@gmail.com> <20191030102531.12495-4-zimon.toutoune@gmail.com> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#37988] [PATCH 4/6] gnu: Add r-cytolib. In-reply-to: <20191030102531.12495-4-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: Wed, 30 Oct 2019 12:41:29 +0100 Message-ID: <87zhhifok6.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: 37988@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: > * gnu/packages/bioconductor.scm (r-cytolib): New variable. [=E2=80=A6] > + (synopsis "C++ infrastructure for representing and interacting > with the gated cytometry") I would remove =E2=80=9Cthe=E2=80=9D from =E2=80=9Cthe gated cytometry=E2= =80=9D. How about =E2=80=9CInfrastructure for working with gated cytometry data=E2=80=9D? > + (description "This package provides the core data structure and API = to > +represent and interact with the gated cytometry data.") Here I=E2=80=99d also remove =E2=80=9Cthe=E2=80=9D. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 07:42:09 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 11:42:09 +0000 Received: from localhost ([127.0.0.1]:49385 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPmMb-0002yW-6v for submit@debbugs.gnu.org; Wed, 30 Oct 2019 07:42:09 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21131) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPmMZ-0002yP-OT for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 07:42:08 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1572435726; cv=none; d=zohomail.com; s=zohoarc; b=KFiS0iGZjjuzzIZQV3QhvZTV7JtT3Ny/wZ+kaELoXOWLUXm69wtGUvrUDmV18QHHXKz8VicFeGs7/ZOKulD+iad407do+vMdGWOt2NblpVv0gn4qgkWEmW534CsyDWqt4u0pj4KynL7onz3Jyo6o7DHfm1Ok4m/tKELOwFG2Tjc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1572435726; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=GDgnicwO3bjM/zwJSyD0lxuQY02VldeDAbrdI+LIDTk=; b=NNmEAcLobd7JNWEOK52OtRKPIJFHzk5QZDz3lVFVtOQF7LxOJECCMliAUUURAsBJAwNWkT/hobMxab0l0BeNL8G3LnZyqXVm/Hw/qqmGHsG6yhPq1YTr7/ib4IibLtnBVicmEIPXWzT2rOM6vHQdcR+46x+mdH1k706kVZ4dijM= 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=1572435726; 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; l=162; bh=GDgnicwO3bjM/zwJSyD0lxuQY02VldeDAbrdI+LIDTk=; b=DcnH7gKCQVF7cvxho7Bid0JJcJivNArTFEBtcWAaZXaF1+mOjfemu5ddL7y1Yua0 zKhRyvEz8a04Wp9i+GlfYfpM4KIpqKa66kdOdkSdhKYD3gREQn7YL/9/lJrFN6TjcQ+ hSuyOz0NsObYIRX0xjG6tGod63DuElRPZyRsE3pc= Received: from localhost (p54AD4E25.dip0.t-ipconnect.de [84.173.78.37]) by mx.zohomail.com with SMTPS id 1572435725449760.5381476573887; Wed, 30 Oct 2019 04:42:05 -0700 (PDT) References: <20191030102531.12495-1-zimon.toutoune@gmail.com> <20191030102531.12495-5-zimon.toutoune@gmail.com> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus To: zimoun Subject: Re: [bug#37988] [PATCH 5/6] gnu: Add r-ncdfflow. In-reply-to: <20191030102531.12495-5-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: Wed, 30 Oct 2019 12:42:02 +0100 Message-ID: <87y2x2foj9.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: 37988@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: > * gnu/packages/bioconductor.scm (r-ncdfflow): New variable. This looks good to me. Thank you! -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 08:42:40 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 12:42:40 +0000 Received: from localhost ([127.0.0.1]:49436 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPnJ9-0008Py-Qk for submit@debbugs.gnu.org; Wed, 30 Oct 2019 08:42:40 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:33534) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPnJ6-0008Pk-HH for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 08:42:38 -0400 Received: by mail-wm1-f51.google.com with SMTP id 6so4221931wmf.0 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 05:42:36 -0700 (PDT) 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=05YbdKMNqRinI6+56YPoE7XS0VxUyqQw1xjIg6DpUl0=; b=Q254oOEBg76yzdsTUPBbZqSMA3iyj9Y6pE3E1/XiR6inezGaIiB4G3T13qCwxdQJKA lZxOOdVS5Sin7DNSngrRt9n/6c5XRm+Wn2b7dJTAfZKEZN8P594ryH7Qnomzll6RRU0u TOqP4ZodgRUdlCLDkEXFYl/TojnD/NZ/xA+D7W6CWPJQ72RRcsN3ZWDHcoK3AIQ7Mbv3 cLQm8q41J4z96pfUus+nnAPeWD5y0rk8bQE14K3eDF5HA3ctaMHYMeL2vcThi1wVUahs bDcyZuXD11jHrLAJL+adcOwmty28PL/7XjfeI/aPESaWGpRgkcWn58r5Ba9ycze0+DJ7 eFbQ== 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=05YbdKMNqRinI6+56YPoE7XS0VxUyqQw1xjIg6DpUl0=; b=n+23uaS+oJ3842GRh9yay+oZx0Garkfj4VAUjApuVHzbGcuXGHz5QDRVXKPTrNsOdg rqYq9ZY0FrQdSve1i+5ui88WYTOIJyvfqkZiHYqA7aZzf0yPNwkCvCR4bHuT2jyGa2ps QFUGv895loBTozp736fX2TJEA6bROlALaUMgO2DU6yQIWyofJgOV6hg/qMD23XKAkfy+ 0B6wv6tCUcje+ulCBJ10cCO/A1ue960DrQKGAxEuvzovco/NWoHY9AibqSyMvB/BCgQC 3RutLpgTeIgo0xD1r/4YQGYeZPQ34kax3PLQcurtxsDYAWzRrCHvojrYpQXZI37sk2lp 4OQg== X-Gm-Message-State: APjAAAUq2+2eaOT0NTODrcOnO+QHXKpcJ/q/lIbHYK5/595SUAnknLJV WzvEBpbi9RxaS+egAxIzV+xPuYvL X-Google-Smtp-Source: APXvYqyc+l22Zxpnemsqxa6h1iPQd0hE8WDp4djTek6uaY1WqXeKy+FuZD6+aTkpoe8P5dbl5epIrQ== X-Received: by 2002:a1c:9d4a:: with SMTP id g71mr9296380wme.66.1572439350380; Wed, 30 Oct 2019 05:42:30 -0700 (PDT) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id s21sm136732wrb.31.2019.10.30.05.42.29 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 30 Oct 2019 05:42:29 -0700 (PDT) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH v2 4/6] gnu: Add r-cytolib. Date: Wed, 30 Oct 2019 13:42:24 +0100 Message-Id: <20191030124224.29391-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <87zhhifok6.fsf@elephly.net> References: <87zhhifok6.fsf@elephly.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-cytolib): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c1761852c..00b10918ff 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6205,3 +6205,26 @@ data.") (description "This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.") (license license:bsd-3))) + +(define-public r-cytolib + (package + (name "r-cytolib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cytolib" version)) + (sha256 + (base32 + "10sdkwrmzmp3sh59hl3x0zxwlw77v80jnv8gz1qrv66skjb764cq")))) + (properties + `((upstream-name . "cytolib"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-rprotobuflib" ,r-rprotobuflib))) + (home-page "https://bioconductor.org/packages/cytolib") + (synopsis "Infrastructure for working with gated cytometry data") + (description "This package provides the core data structure and API to +represent and interact with gated cytometry data.") + (license license:artistic2.0))) -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 30 09:29:39 2019 Received: (at 37988) by debbugs.gnu.org; 30 Oct 2019 13:29:39 +0000 Received: from localhost ([127.0.0.1]:49512 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPo2d-00038N-4k for submit@debbugs.gnu.org; Wed, 30 Oct 2019 09:29:39 -0400 Received: from mail-qt1-f196.google.com ([209.85.160.196]:36824) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iPo2a-00038A-J6 for 37988@debbugs.gnu.org; Wed, 30 Oct 2019 09:29:38 -0400 Received: by mail-qt1-f196.google.com with SMTP id x14so3210623qtq.3 for <37988@debbugs.gnu.org>; Wed, 30 Oct 2019 06:29:36 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=3vYCReCcay5qYsXx66BQHzrNWdkalsOuQ9jQKfiNvc4=; b=b+yKMTSCLuZWNfSjuQe44TUr7CdZbxKgsprcRLkWATpmt3t++9pD29dod5wMN2d0zi Y0ZUXWpRW6GeX7QtRV9j3Mr58uZ8BB39qkFup6A5HyhtvPp+XqQUofn59/5AE/oS+Hbg sxu6p5MxZLgS17vIHIOAtZldhQNq8GW/uymnV/z3/cld2gEtI36WzxLNfdWwSlCLaJ5v bPoZ5ZjDerrFGn2ybFzugBgcO5DoyWTKN+4ma6g5IVaKYVaJs4F6MsEorDXYKGPqg8uJ rKQXxlrRJydeB6nye0Bv86VvlwAHOUqhEzLEFR+GzAI5SuyMgTx7gUnBeHmf+LhUSjV7 kh5w== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=3vYCReCcay5qYsXx66BQHzrNWdkalsOuQ9jQKfiNvc4=; b=ue/9Z6YrFZ+j4xrtYbu9KxzwOOXZKInRtbj/L58UudaDAbu3DHS4CyWbH7SiuKhTBy tQcpDtasqaaWmiGCtN4nhghdan7KVZ+j9qDB/97g3iEEXPiIjM6x78I7kN1BcRfngCNL TaPBG3HkZz0sik3N0oKJUNVkqOy3tlAc9s1EY72/bHZA5q5zFDZFKIL8qh4YFtGVECCu J4pHN879ZJindisXeHXXEpFq5xq6QyXHxU/iz1glhc3JS7r0ZJjzJDTr2HVo2JqQeSn4 xu6JPCe9Ri42xEUlEkGIkJUe1/pUJpfSg5aXZtiUBtDuI8tD0hudgrzweAVPx6tbjQv6 mViw== X-Gm-Message-State: APjAAAUqDB25z3RYmEQcjC86FJqX7D6Z3gBtYPUUAioCrdGq0ALjMvfA A0Wj6bVtDEqVAmZJPgCQCGYysqIzUrMbkcSGVG0AOw== X-Google-Smtp-Source: APXvYqzXBSgRG2p6Zgc2zUSvZqRC3MEavUkfOvTmX77oVophrHb588Hs5FM3K31akuCxQjrtJro92hFY5mpxt9rZPi4= X-Received: by 2002:ad4:53a7:: with SMTP id j7mr28111196qvv.77.1572442170906; Wed, 30 Oct 2019 06:29:30 -0700 (PDT) MIME-Version: 1.0 References: <20191030102531.12495-1-zimon.toutoune@gmail.com> <20191030102531.12495-3-zimon.toutoune@gmail.com> <8736fah38i.fsf@elephly.net> In-Reply-To: <8736fah38i.fsf@elephly.net> From: zimoun Date: Wed, 30 Oct 2019 14:29:19 +0100 Message-ID: Subject: Re: [bug#37988] [PATCH 3/6] gnu: Add r-rprotobuflib. To: Ricardo Wurmus Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: 37988@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 (-) Hi Ricardo, Thank you for reviewing. On Wed, 30 Oct 2019 at 12:39, Ricardo Wurmus wrote: > > * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable. > > > + (arguments > > + `(#:phases > > + (modify-phases %standard-phases > > + ;; Contains unverified binaries: > > + ;; src/win/lib/{i386,x64}/libprotobuf.a > > + (add-after 'unpack 'remove-win-folder > > + (lambda _ > > + (delete-file-recursively "src/win") > > + #t)) > > This should be done in a snippet instead. What does it mean? > > + ;; Fix non-conventional packaging. > > + ;; The dependency to protobuf-2.6.0 is included as tgz and build > > + ;; by the R package itself. > > + (add-after 'unpack 'fix-wrong-hard-coded > > + (lambda _ > > + (with-directory-excursion "src" > > + (invoke "tar" "xf" "protobuf-2.6.0.tgz")) > > + (substitute* "src/protobuf-2.6.0/configure" > > + (("#! /bin/sh") (string-append "#!" (which "sh")))) > > + #t))))) > Can we just use our protobuf package instead of using the bundled sources? I do not know and I have not tried yet. The package claims the dependency to 2.6.0 and we do not have this one. As said in the cover letter to these patches, we could patch to correctly package without the bundle source and this is IMHO the way to go. However it is more work and it is better to have the package available than no package at all. Well, I will give another look to see if a quick improvement can be done. :-0 All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Tue Nov 05 12:49:17 2019 Received: (at 37988) by debbugs.gnu.org; 5 Nov 2019 17:49:17 +0000 Received: from localhost ([127.0.0.1]:39036 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS2xB-0004U0-6U for submit@debbugs.gnu.org; Tue, 05 Nov 2019 12:49:17 -0500 Received: from mail-wr1-f44.google.com ([209.85.221.44]:44304) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS2x8-0004Ti-CG for 37988@debbugs.gnu.org; Tue, 05 Nov 2019 12:49:15 -0500 Received: by mail-wr1-f44.google.com with SMTP id f2so13575130wrs.11 for <37988@debbugs.gnu.org>; Tue, 05 Nov 2019 09:49:14 -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=m/uxBZiuhFZSsXbRVA6CfX2Y2RluSIrAgErcE9OtoBM=; b=dwSA7DEFXVn5pWgWar2jbnz6CMHqjbNK8JZfcY/D1gerZ9VtjGCmVxsetJfGZXg1uG PGjhtbSonWPoOxOdVToajY/CW6EVfTjOuZmAhFzPTmepI/ymj2UYe2gpVb23V6lcfuJE NWrk6gsiU8N7NPnnFZACCM0dcDjAPcd1W0W9Ep+FnXrele9SIK/eUmawQc/9ZfCOH/lz mufvNTx0H9YgVxHINofxmMUNoJUpFTuEB+POwp+Teb0WqzkVDM7HGC5AKq6Cd+cmkK9S imOuR1r0x7yA7ofR06rPtXiqVl8Tl05aSvRrxvtGDBeGATbYQMx+JvcLYLh4hMUITdNK kOUg== 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=m/uxBZiuhFZSsXbRVA6CfX2Y2RluSIrAgErcE9OtoBM=; b=Z58RGCLM5ZoiOgVL0t5UgbXx0ey4L1yB4mDH41ehqXT8ox1GfodK0JeksGLi80tZIg 3xS8s56aYjHoEoCO8ejqXzFUgMZ1CLVGnzYmV2Pg90dUrLtXb57PhYN8EVmjw8O1OmNj B7+7keUnl/fvMrQjWCpgyAN2oZ8px1Oj/48vtjsJzNVZdNJLb1K3cPVVcTeIdwN4G4R5 SPqCnOoPSfN3kDWTegP6Jbw0B3ZJ9gtRUADv0Xxl4Jq2utshzPHu2kiPdSV45UWyPYlf kx6Eob1ioCMai78EDKSxyuvnrQnBD1KDhqw0Jq0qzo0l8fuqFfdhWxdaES8+tmL0GL7P 6CPQ== X-Gm-Message-State: APjAAAUyY1jdTfJw6glok8iLrFpvuM5vdyJAoF+Ck0N7KVkz+Qgu6i+N 8O6TWTTABaBk+FI/kdyKIMtv+vM4 X-Google-Smtp-Source: APXvYqwpR1GykR8sMWvBOhQB5PsVXADIwrrzzMs2AJEAiLHVX9pBky59ZQcHe08EZ6nylLz4KBJtDw== X-Received: by 2002:adf:db92:: with SMTP id u18mr11683107wri.1.1572976148138; Tue, 05 Nov 2019 09:49:08 -0800 (PST) Received: from pfiuh02.univ-paris-diderot.fr ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id z15sm21070467wrr.19.2019.11.05.09.49.07 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 05 Nov 2019 09:49:07 -0800 (PST) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH v2 3/6] gnu: Add r-rprotobuflib. Date: Tue, 5 Nov 2019 18:49:00 +0100 Message-Id: <20191105174900.25449-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable. * gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch: New file. --- gnu/packages/bioconductor.scm | 31 ++++++++++ .../r-rprotobuflib-unbundle-dependency.patch | 57 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92e5d3ec0b..5a6d629939 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web) + #:use-module (gnu packages protobuf) #:use-module (srfi srfi-1)) @@ -6166,3 +6167,33 @@ data.") (synopsis "Visualization for flow cytometry data") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) + +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg")) + ;; Remove bundled binaries: + ;; src/win/lib/{i386,x64}/libprotobuf.a + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "src/win") + #t)) + (patches + (search-patches "r-rprotobuflib-unbundle-dependency.patch")))) + (properties + `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (propagated-inputs + `(("protobuf-2" ,protobuf-2))) + (home-page "https://bioconductor.org/packages/RProtoBufLib") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description "This package provides the headers and static library of +Protocol buffers 2.6.0 for other R packages to compile and link against.") + (license license:bsd-3))) diff --git a/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch new file mode 100644 index 0000000000..c26b6c7e0f --- /dev/null +++ b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch @@ -0,0 +1,57 @@ +diff --git a/configure b/configure +index 7edae5f..eff2489 100755 +--- a/configure ++++ b/configure +@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex + ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + +-#untar the lib +-BASEPBNAME="protobuf-2.6.0" +-PBTGZNAME=${BASEPBNAME}.tgz +-cd src +-if test -d ./${BASEPBNAME}; then +- echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.' +-else +- echo "untarring protobuf ..."; +- gunzip -dc ${PBTGZNAME} | tar xf -; +-fi; +- +-#run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... ) +-cd ${BASEPBNAME} +-#./autogen.sh +-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf +-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename +-cd .. +- +-echo "building protobuf..."; +-PBBUILD=$(pwd)/pb_build +-if test -d ${PBBUILD}; then +- echo 'found ' $PBBUILD ' ;using what is there.' +-else +- mkdir ${PBBUILD} +-fi; +- +-cd ${BASEPBNAME}; +-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}" +-$MAKE install +- +-cd ../../ +- +- + + + ac_config_files="$ac_config_files src/Makevars" +diff --git a/src/Makevars.in b/src/Makevars.in +index 63803fb..575d507 100644 +--- a/src/Makevars.in ++++ b/src/Makevars.in +@@ -10,9 +10,6 @@ all: copying + + #copy hdf5 library headers to package include + copying: $(GS_LIB) +- mkdir -p "${USER_INCLUDE}" +- cp -r @PBBUILD@/include/google ${USER_INCLUDE} + mkdir -p "${USER_LIB_DIR}" +- cp @PBBUILD@/lib/* ${USER_LIB_DIR} + cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Nov 05 13:20:08 2019 Received: (at 37988) by debbugs.gnu.org; 5 Nov 2019 18:20:08 +0000 Received: from localhost ([127.0.0.1]:39057 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS3R0-0005Mt-0v for submit@debbugs.gnu.org; Tue, 05 Nov 2019 13:20:06 -0500 Received: from mail-wr1-f42.google.com ([209.85.221.42]:37340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS3Qx-0005M8-Jd for 37988@debbugs.gnu.org; Tue, 05 Nov 2019 13:20:04 -0500 Received: by mail-wr1-f42.google.com with SMTP id t1so16666608wrv.4 for <37988@debbugs.gnu.org>; Tue, 05 Nov 2019 10:20:03 -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=D9hXoHnqI4wIlwZ6yrF/KI6ZimwfshrfxxJ8+Z8P1DI=; b=scxagQw9neWGQ2bSccWu9B9SbwZm67HrRfigePgDKR9IgWXoBCjrowNa3wPpsyyUHc X/f6KHUvcl+7PQlGIz1c0ZS6pKzfZO+UW5jc4Hq0DHy+IyaowuhIylPuAh0Mtf7OaYTO kQbgNl6mQGDIJYMqM3aUD5OK6jnXRFIYnw7CZEfhGh23PPDOed5POG0RG/Y4x3OxMc/5 e5lF4ZaZISbQLnsx1M7aiGTZixZsqrhPdS1ndADvbZgRhMNoQ0DJN6YN7dc2wmq1Vwk7 wJFxTQ0rily42YmYSN0gVqcRz1RyGQOlr8ZwgCSCOMwcKOqYPUqb+6Bbutr6/Ir/KDn0 XGGg== X-Google-DKIM-Signature: v=1; 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Tue, 05 Nov 2019 10:19:56 -0800 (PST) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH v3 3/6] gnu: Add r-rprotobuflib. Date: Tue, 5 Nov 2019 19:19:54 +0100 Message-Id: <20191105181954.26339-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <8736fah38i.fsf@elephly.net> References: <8736fah38i.fsf@elephly.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable. * gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch: New file. --- gnu/packages/bioconductor.scm | 31 ++++++++++ .../r-rprotobuflib-unbundle-dependency.patch | 57 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92e5d3ec0b..801e52245b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -38,6 +38,7 @@ #:use-module (gnu packages netpbm) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages protobuf) #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (srfi srfi-1)) @@ -6166,3 +6167,33 @@ data.") (synopsis "Visualization for flow cytometry data") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) + +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg")) + ;; Remove bundled binaries: + ;; src/win/lib/{i386,x64}/libprotobuf.a + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "src/win") + #t)) + (patches + (search-patches "r-rprotobuflib-unbundle-dependency.patch")))) + (properties + `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (propagated-inputs + `(("protobuf-2" ,protobuf-2))) + (home-page "https://bioconductor.org/packages/RProtoBufLib") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description "This package provides the headers and static library of +Protocol buffers for other R packages to compile and link against.") + (license license:bsd-3))) diff --git a/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch new file mode 100644 index 0000000000..c26b6c7e0f --- /dev/null +++ b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch @@ -0,0 +1,57 @@ +diff --git a/configure b/configure +index 7edae5f..eff2489 100755 +--- a/configure ++++ b/configure +@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex + ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + +-#untar the lib +-BASEPBNAME="protobuf-2.6.0" +-PBTGZNAME=${BASEPBNAME}.tgz +-cd src +-if test -d ./${BASEPBNAME}; then +- echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.' +-else +- echo "untarring protobuf ..."; +- gunzip -dc ${PBTGZNAME} | tar xf -; +-fi; +- +-#run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... ) +-cd ${BASEPBNAME} +-#./autogen.sh +-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf +-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename +-cd .. +- +-echo "building protobuf..."; +-PBBUILD=$(pwd)/pb_build +-if test -d ${PBBUILD}; then +- echo 'found ' $PBBUILD ' ;using what is there.' +-else +- mkdir ${PBBUILD} +-fi; +- +-cd ${BASEPBNAME}; +-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}" +-$MAKE install +- +-cd ../../ +- +- + + + ac_config_files="$ac_config_files src/Makevars" +diff --git a/src/Makevars.in b/src/Makevars.in +index 63803fb..575d507 100644 +--- a/src/Makevars.in ++++ b/src/Makevars.in +@@ -10,9 +10,6 @@ all: copying + + #copy hdf5 library headers to package include + copying: $(GS_LIB) +- mkdir -p "${USER_INCLUDE}" +- cp -r @PBBUILD@/include/google ${USER_INCLUDE} + mkdir -p "${USER_LIB_DIR}" +- cp @PBBUILD@/lib/* ${USER_LIB_DIR} + cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Nov 05 13:29:52 2019 Received: (at 37988) by debbugs.gnu.org; 5 Nov 2019 18:29:52 +0000 Received: from localhost ([127.0.0.1]:39065 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS3aM-0005d2-7K for submit@debbugs.gnu.org; Tue, 05 Nov 2019 13:29:50 -0500 Received: from mail-wr1-f48.google.com ([209.85.221.48]:44365) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1iS3aF-0005ci-Lz for 37988@debbugs.gnu.org; Tue, 05 Nov 2019 13:29:43 -0500 Received: by mail-wr1-f48.google.com with SMTP id f2so13723856wrs.11 for <37988@debbugs.gnu.org>; Tue, 05 Nov 2019 10:29:39 -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=mznVtSH1nnVDLZJDsXRVgZfVOiYcZ1VVp/3Z4S1aTow=; b=RVLICf2f3LjhC8KZ/m69gzk9gMNxwjPxrP8+HSH/c7+bqOJTv8+VbEDYG8xgDyDw3A It+4ahYbiKQhvv1DBDVQykvFWFeu/nJi5LpnzrYIqSaH2xlavz6IcOtksBSJ0Fh8d+Ox oUfBjfjcQKpxL/wznOlYo8IFiCg50sYiu79iLuUG3Z5b4jbWEmw/mc/PY+CAiBDLWGEV OGxtNgSJaH7pRCOxF5m+01bEv8ZPVrkttx5fQHNBujghWnKI4t9AUtJU7dXAXyov39oY UtlL3t1NDMo/2R8KE51gqBv/oWmS3tXHd1TVtHVTm+VFtbbCjq+7b5kHISR7bIAzmNgA tzbQ== X-Google-DKIM-Signature: v=1; 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Tue, 05 Nov 2019 10:29:32 -0800 (PST) From: zimoun To: 37988@debbugs.gnu.org Subject: [PATCH v4 3/6] gnu: Add r-rprotobuflib. Date: Tue, 5 Nov 2019 19:29:31 +0100 Message-Id: <20191105182931.27048-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.23.0 In-Reply-To: <8736fah38i.fsf@elephly.net> References: <8736fah38i.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: zimoun X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-rprotobuflib): New variable. * gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch: New file. --- gnu/local.mk | 2 + gnu/packages/bioconductor.scm | 31 ++++++++++ .../r-rprotobuflib-unbundle-dependency.patch | 57 +++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5b81791542..178c8b903f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -22,6 +22,7 @@ # Copyright © 2018 Maxim Cournoyer # Copyright © 2019 Guillaume Le Vaillant # Copyright © 2019 John Soo +# Copyright © 2019 Simon Tournier # # This file is part of GNU Guix. # @@ -1295,6 +1296,7 @@ dist_patch_DATA = \ %D%/packages/patches/quagga-reproducible-build.patch \ %D%/packages/patches/quickswitch-fix-dmenu-check.patch \ %D%/packages/patches/qtwebkit-pbutils-include.patch \ + %D%/packages/patches/r-rprotobuflib-unbundle-dependency.patch \ %D%/packages/patches/randomjungle-disable-static-build.patch \ %D%/packages/patches/rapicorn-isnan.patch \ %D%/packages/patches/rapidjson-gcc-compat.patch \ diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 92e5d3ec0b..801e52245b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -38,6 +38,7 @@ #:use-module (gnu packages netpbm) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages protobuf) #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (srfi srfi-1)) @@ -6166,3 +6167,33 @@ data.") (synopsis "Visualization for flow cytometry data") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) + +(define-public r-rprotobuflib + (package + (name "r-rprotobuflib") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RProtoBufLib" version)) + (sha256 + (base32 + "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg")) + ;; Remove bundled binaries: + ;; src/win/lib/{i386,x64}/libprotobuf.a + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "src/win") + #t)) + (patches + (search-patches "r-rprotobuflib-unbundle-dependency.patch")))) + (properties + `((upstream-name . "RProtoBufLib"))) + (build-system r-build-system) + (propagated-inputs + `(("protobuf-2" ,protobuf-2))) + (home-page "https://bioconductor.org/packages/RProtoBufLib") + (synopsis "C++ headers and static libraries of Protocol buffers") + (description "This package provides the headers and static library of +Protocol buffers for other R packages to compile and link against.") + (license license:bsd-3))) diff --git a/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch new file mode 100644 index 0000000000..c26b6c7e0f --- /dev/null +++ b/gnu/packages/patches/r-rprotobuflib-unbundle-dependency.patch @@ -0,0 +1,57 @@ +diff --git a/configure b/configure +index 7edae5f..eff2489 100755 +--- a/configure ++++ b/configure +@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex + ac_compiler_gnu=$ac_cv_cxx_compiler_gnu + + +-#untar the lib +-BASEPBNAME="protobuf-2.6.0" +-PBTGZNAME=${BASEPBNAME}.tgz +-cd src +-if test -d ./${BASEPBNAME}; then +- echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.' +-else +- echo "untarring protobuf ..."; +- gunzip -dc ${PBTGZNAME} | tar xf -; +-fi; +- +-#run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... ) +-cd ${BASEPBNAME} +-#./autogen.sh +-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf +-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename +-cd .. +- +-echo "building protobuf..."; +-PBBUILD=$(pwd)/pb_build +-if test -d ${PBBUILD}; then +- echo 'found ' $PBBUILD ' ;using what is there.' +-else +- mkdir ${PBBUILD} +-fi; +- +-cd ${BASEPBNAME}; +-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}" +-$MAKE install +- +-cd ../../ +- +- + + + ac_config_files="$ac_config_files src/Makevars" +diff --git a/src/Makevars.in b/src/Makevars.in +index 63803fb..575d507 100644 +--- a/src/Makevars.in ++++ b/src/Makevars.in +@@ -10,9 +10,6 @@ all: copying + + #copy hdf5 library headers to package include + copying: $(GS_LIB) +- mkdir -p "${USER_INCLUDE}" +- cp -r @PBBUILD@/include/google ${USER_INCLUDE} + mkdir -p "${USER_LIB_DIR}" +- cp @PBBUILD@/lib/* ${USER_LIB_DIR} + cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o -- 2.23.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 11:40:06 2020 Received: (at 37988) by debbugs.gnu.org; 21 Feb 2020 16:40:07 +0000 Received: from localhost ([127.0.0.1]:47922 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BLS-0007RB-OQ for submit@debbugs.gnu.org; Fri, 21 Feb 2020 11:40:06 -0500 Received: from mail-qt1-f196.google.com ([209.85.160.196]:37716) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BLR-0007Qe-FJ for 37988@debbugs.gnu.org; Fri, 21 Feb 2020 11:40:05 -0500 Received: by mail-qt1-f196.google.com with SMTP id w47so1701277qtk.4 for <37988@debbugs.gnu.org>; Fri, 21 Feb 2020 08:40:05 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=8BRpqt4rU0rDhl7ACcyt9wZpuP7FKEEgaMtvlNonRoo=; b=MarizxEkQFxphJvbykxvijOPe2BwS+1TGYtls4xq1jRAeR9JdVIsjGex9lxoYK194s jKvmQb3+ah1QZuWXUQCER0W69V77telLA6g1m9bWcWyWvdbmnlnkRIpP8Ep1xS+0eNty g+/wbIrCm/Yp7wfk8xp6XbNij3Ev1hkq/y7Bc45LfTdrB1vDQZG9GbKQ8ukAGdFt3lIP 9o9S6Rb52XD2m/nt3cqzGErhhdbuwe/DsSuXGIFfz6E48rC9jF2aYgKdgxEPpgh57Hap IVBEUXEw2kdVpo8GO9CH3RPHJsh09smh2oMxLWEHAFxJXR+NAtUa1STvVAqSisz4cM37 cWFg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=8BRpqt4rU0rDhl7ACcyt9wZpuP7FKEEgaMtvlNonRoo=; b=sFgpVEjxX3FCyH8yPUah08WyUKqxiHb4udfqUQs/xQlR/jE9tovFecUs8yzQ619QXX SWcGYDuY2kmpN/sTXUOge21/xf28VzKxuMdZBunApOVTdyt5xXVZCGhI57hSt6tXBAOo 4DC8viQBjWXj77DmsjljkU+JaOtl4bMP99ARrRVYjzu155YfYIQ8+jf2h/z8tcvI67oi SWer+ei1kZIkTnYoI17boX1VoWI48BQzY1pk4ndYK10YuBD2gYJJtF32CodoPJhXWue+ U2vq4SxoeJf5HHdwLpzkCJ9RFvi0XpPJ3ySnHuACMZ7aVIpaetgnXPH10e2AhPNFkFmT cCOA== X-Gm-Message-State: APjAAAXhzCcZE2NqzBiDqV3BekjD21i2FVA74VkDBv002jbOwK2dY8BU FAiUnC6gur4YuwKLgV6jOwYABe+h6lvv1dabgf85IxAc X-Google-Smtp-Source: APXvYqyBs+Cwfgkd97/SuLy5bSHP/zcgnl0rXmvWh0BTY6Nu3hvXJPAFszXik2mYFZgziUv46/iGwrRWzXXbEP+eHFY= X-Received: by 2002:ac8:6bc1:: with SMTP id b1mr31691134qtt.313.1582303199745; Fri, 21 Feb 2020 08:39:59 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 17:39:48 +0100 Message-ID: Subject: why? To: 37988@debbugs.gnu.org, Ricardo Wurmus Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 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, Why did you pushed your commits instead of mines? Especially when they had not fallen in the crack. I sent them the October 30, 2019. https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988 And you commented them the same day: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#26 I modified one the November 5th, 2019: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=37988#47 And you committed and pushed the same packages on the December, 15th. Cheers, simon From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 11:41:45 2020 Received: (at control) by debbugs.gnu.org; 21 Feb 2020 16:41:45 +0000 Received: from localhost ([127.0.0.1]:47927 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BN3-0007U3-2B for submit@debbugs.gnu.org; Fri, 21 Feb 2020 11:41:45 -0500 Received: from mail-qt1-f178.google.com ([209.85.160.178]:41004) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5BMz-0007Tj-WB for control@debbugs.gnu.org; Fri, 21 Feb 2020 11:41:43 -0500 Received: by mail-qt1-f178.google.com with SMTP id l21so1689469qtr.8 for ; Fri, 21 Feb 2020 08:41:41 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:from:date:message-id:subject:to; bh=BkTuav2Y7pzmzu8J3Y07LRqfVlsQ1nSJt6qFhhtZmaY=; b=jipYTn/X5X3BV21YBWyj/IBJKdB/KJ5YdocMbGse00Ih2eaiYZw9GiHZM8ntGxkKHp xTm5npTtatMUnJRn38/IAnhYV9Q0bm5tqMQujmiSi3I0AShwBafEB/jLsLIRY+d/Ek1Y 8ijC72fjVDb4ZGQEAXsctWfTveR21p2bZV7rm6K6AWC3iKSTbpTLjZmwMzDo7gsssFVw wEMlDz3xsCvYQKaoxAVL9EOszDxtWlcZgJLTLBInQPVLEmvrRIiB4n5A5MthxJzBvpxD BCpsPf/yVWXekv09PDNyQPfzXPhf+zI+uqZIUWW+6E5DCR6dgumFd2vtyyHNlyX8Fm0A MhwA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=BkTuav2Y7pzmzu8J3Y07LRqfVlsQ1nSJt6qFhhtZmaY=; b=Dpm86T2quvRcrkV1pHQ24ijN6EFvgdytADLBT0EIp/Xo8YRkL91KpD5t+FAmt2osD4 XXR3B79h0XT+RSk8/RsqCzSWqhIIm5KiD7qgqQCY1DEcmLKURFYb1xwZWqcDX4Cn5eG/ ooIJ6XyTYwz0KcHucTRRSRyzY/R2mhWIyN60aBQjaRFWKZhTR83xVerzoEnOu7MFkRJv Og5wtmumrFX/3vrV6EUaaOMzmJtktkxJ1skHfebWHJcRzvKitZQnSblvKqaEzYje42WR fJusZ40SK+TVrVU8oM0YGhMODQscprL1iLcAx9CBGRfOpiItYwbVzdkf6vWquAmiDGrK h+aQ== X-Gm-Message-State: APjAAAXy9THaIESJ/r2DwT7LDMpD2eqj6noULZz3QB31kuBsLncBHccz 1HULKm01Sb3KUXry9bveK3ZIkFfh6EHmUnvETMhjhA== X-Google-Smtp-Source: APXvYqwCbSPlVODXbsvjSRMQpcPI/3ZU8XYijXVQ5LX2RIU5IfqsGgKxzdep7670ZufOUTBuc0OP56eeD6dZ4Y3cpeM= X-Received: by 2002:aed:2050:: with SMTP id 74mr32546353qta.217.1582303295312; Fri, 21 Feb 2020 08:41:35 -0800 (PST) MIME-Version: 1.0 From: zimoun Date: Fri, 21 Feb 2020 17:41:24 +0100 Message-ID: Subject: packages already pushed To: control@debbugs.gnu.org Content-Type: text/plain; charset="UTF-8" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: control X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) close 37988 thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 13:39:03 2020 Received: (at 37988) by debbugs.gnu.org; 21 Feb 2020 18:39:03 +0000 Received: from localhost ([127.0.0.1]:48104 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DCZ-00083y-6W for submit@debbugs.gnu.org; Fri, 21 Feb 2020 13:39:03 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21103) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DCW-00083W-R1 for 37988@debbugs.gnu.org; Fri, 21 Feb 2020 13:39:01 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1582310339; cv=none; d=zohomail.com; s=zohoarc; b=Z9/J0xhh+Q8E6q40G07jrBy/b+3pPGpHFtFIIuOU8Mribk0/WG+EBy+m5eIjqsiTddoFMRWz4JYWJYgYZtGez2YVpMQ2HW184uXdgPmVrLj647lsJVN6K2SUvSB0fm7QOT0R9lbsB/lr4LZmt2VmkpSGw/hLVekP9DZuPTj2jP0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1582310339; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=aYGAzLd6szwjbtU2tgSvLKuF/QBMgL2oc7bSc7ikxco=; b=GF4wGmX3x+ShUWsh39KSRjtkDqmxdGk5CTPEEZhCsdDSKVirKehj98T/xnXSeVVTIbehmOEm4jDeSSqg92+QU3GYOHlUtyAojiG3TxthJ70YhlSA7fdA43Yoewnip+7xMNhUoylv1qIfWH72E1SxWDjQc2snBDA1pfvlUfiMfuQ= 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=1582310339; 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:Content-Transfer-Encoding; bh=aYGAzLd6szwjbtU2tgSvLKuF/QBMgL2oc7bSc7ikxco=; b=IltSg2TrIiCniLIewwX38IYn88ixJ9ksjlAdGGDcVXCuIla4ra9gAKSn/0J4bg5z THxIHGhrueodDhy1wbncI46a3rNBgMl63PcD+L+AmxNJxHYOCqpCQx+JfejFDv8xFtS Gj7BvjH4lBF4/6how0ByN+Ii6+w3Euup5aPXhPGk= Received: from localhost (p54AD4D13.dip0.t-ipconnect.de [84.173.77.19]) by mx.zohomail.com with SMTPS id 1582310337006341.64979955848617; Fri, 21 Feb 2020 10:38:57 -0800 (PST) References: User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus To: zimoun Subject: Re: why? In-reply-to: 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: Fri, 21 Feb 2020 19:38:53 +0100 Message-ID: <87blprlr9e.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: 37988@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 (-) Hi, > Why did you pushed your commits instead of mines? > Especially when they had not fallen in the crack. > > I sent them the October 30, 2019. > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D37988 > > And you commented them the same day: > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D37988#26 > > I modified one the November 5th, 2019: > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D37988#47 Uh, that=E2=80=99s odd. I remember working with your r-flow* patches. I d= id not have my own versions of these patches. I know this because I had not previously encountered flow cytometry. (I don=E2=80=99t specifically remember r-rprotobuflib from this series.) My guess is that I wasn=E2=80=99t able to apply them cleanly, so I copy & p= asted the diff, adjusted as needed, and then forgot to override the commit author before pushing :-( December is a blur. It=E2=80=99s quite possible that I didn=E2=80=99t work= on the patches all in one go, got interrupted, and then pushed them together with some other work (I see that there are R update commits after these pushes). I=E2=80=99m very sorry to have messed up the authorship here. This was definitely not intended :( -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Fri Feb 21 14:13:05 2020 Received: (at 37988) by debbugs.gnu.org; 21 Feb 2020 19:13:05 +0000 Received: from localhost ([127.0.0.1]:48141 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DjV-0000Tc-FK for submit@debbugs.gnu.org; Fri, 21 Feb 2020 14:13:05 -0500 Received: from mail-qv1-f49.google.com ([209.85.219.49]:44787) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j5DjT-0000T7-1Y for 37988@debbugs.gnu.org; Fri, 21 Feb 2020 14:13:03 -0500 Received: by mail-qv1-f49.google.com with SMTP id n8so1442393qvg.11 for <37988@debbugs.gnu.org>; Fri, 21 Feb 2020 11:13:03 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc:content-transfer-encoding; bh=D/ZNhemPzn8hLh/QxtKkmsRvhllF3HLMZQGrf0S0Ylw=; b=G7GxtRpOfA5ws39dEwkkX4g9fC4wgU0hCZR5upNZapPFb8Gu66jXsIJOwnnugu37o/ abwPmrMLTTh8BmW4R9hy5plv2zwJ4Tz6SiY7f0oc/WNRUgnhR5wxHo3z+i6V9ZjuR/dE zBi6DYzMfOVFuYniGPgwhn3JXm7XN1MtJq2zEptpoZB2194l41mWtI+QbEO/NcWb5yhb QBDruk+prZ/8x4tOkYM9G7y12gHwJeQzKk+ryolcr9YWPfFng6flRRMXjESSB2R/IRyt 6DLsADsJIzXM+JJmPmajndwQldUE7hTUvNJPq7KBzy2sg74Oz6d8pZZ9KoqL+9li2gNR LIrg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc:content-transfer-encoding; bh=D/ZNhemPzn8hLh/QxtKkmsRvhllF3HLMZQGrf0S0Ylw=; b=s/sr4g/QZwdTz5flhZ5cZ8isJ9pLC3Xkk4MbKfHrVGztooYE+88ikJYRb/3K87fpx4 2a6jXm5ulOdKaIxCaryvf19JbCWKYIffiFmzi57xB9Bq4Xm8K818xG7zATAz/yOkhDeQ MGOoz8Jkmm8DEWn/yDOSLlhbDdrFHpX9dT5yNxg+8P3boe3v6neZd51l2lKx2Ve9T0iF JxWGW0nk0tRwWAwKffrgGGS+1m8VkE8CPCOZ5v0sUDWWvhlC4aEamhRqa0TI1+hFzv8A w+oRjmVFtZGDlFxI041YsxOdYitALXFsJHwMVtMmkWeUqlVvGnT59VbclJ7X+GkcrI3T +PEw== X-Gm-Message-State: APjAAAV597YbgYjUD4UsMrk0L8yF6P1i+5VgmNH0VVqZXTVUFNf8QmZf EMfvTn6gM07aASIXyt+1M3QDHBpqlJVJQS40OTA= X-Google-Smtp-Source: APXvYqxHYe6l/70LN1En3QAKcMqMagkcfUHCc90PDAIQrpbUdIEN+/RtmvI7P6KzZNRxMxadWokrFZ5XC8XwPlK0gD0= X-Received: by 2002:a05:6214:3a1:: with SMTP id m1mr30699740qvy.77.1582312377533; Fri, 21 Feb 2020 11:12:57 -0800 (PST) MIME-Version: 1.0 References: <87blprlr9e.fsf@elephly.net> In-Reply-To: <87blprlr9e.fsf@elephly.net> From: zimoun Date: Fri, 21 Feb 2020 20:12:46 +0100 Message-ID: Subject: Re: why? To: Ricardo Wurmus Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 37988 Cc: 37988@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 (-) Hi Ricardo, On Fri, 21 Feb 2020 at 19:39, Ricardo Wurmus wrote: > > Why did you pushed your commits instead of mines? > > Especially when they had not fallen in the crack. > > > > I sent them the October 30, 2019. > > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D37988 > > > > And you commented them the same day: > > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D37988#26 > > > > I modified one the November 5th, 2019: > > https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D37988#47 > > Uh, that=E2=80=99s odd. I remember working with your r-flow* patches. I= did > not have my own versions of these patches. I know this because I had > not previously encountered flow cytometry. (I don=E2=80=99t specifically > remember r-rprotobuflib from this series.) That's why I found weird the twist. :-) I thought I did something unexpected and/or there was a special motivation. And so my "why?". :-) > My guess is that I wasn=E2=80=99t able to apply them cleanly, so I copy &= pasted > the diff, adjusted as needed, and then forgot to override the commit > author before pushing :-( > I=E2=80=99m very sorry to have messed up the authorship here. This was > definitely not intended :( I am ok about the authorship; my salary does not depend on the number of commits accepted. ;-) The most important is that the packages end in Guix; who committed them is less important. Thanks, simon From unknown Sun Aug 17 01:22:14 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 21 Mar 2020 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator