From patchwork Fri Oct 13 15:57:14 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 54812 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 2DF8227BBE2; Fri, 13 Oct 2023 16:59:12 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.6 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED,URIBL_SBL_A autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 467A427BBE9 for ; Fri, 13 Oct 2023 16:59:10 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qrKYj-0003jT-8T; Fri, 13 Oct 2023 11:58:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qrKYh-0003it-EU for guix-patches@gnu.org; Fri, 13 Oct 2023 11:58:39 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qrKYh-0007iQ-6d for guix-patches@gnu.org; Fri, 13 Oct 2023 11:58:39 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qrKZ4-0007tX-85 for guix-patches@gnu.org; Fri, 13 Oct 2023 11:59:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66527] [PATCH 1/2] gnu: Remove r-tgstat. Resent-From: "Afkhami, Navid" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Oct 2023 15:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 66527 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 66527@debbugs.gnu.org Cc: "Afkhami, Navid" X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169721269030186 (code B ref -1); Fri, 13 Oct 2023 15:59:02 +0000 Received: (at submit) by debbugs.gnu.org; 13 Oct 2023 15:58:10 +0000 Received: from localhost ([127.0.0.1]:47237 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qrKYD-0007qo-KH for submit@debbugs.gnu.org; Fri, 13 Oct 2023 11:58:09 -0400 Received: from lists.gnu.org ([2001:470:142::17]:35358) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qrKY9-0007qE-Lm for submit@debbugs.gnu.org; Fri, 13 Oct 2023 11:58:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qrKXh-0003fW-AX for guix-patches@gnu.org; Fri, 13 Oct 2023 11:57:37 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qrKXf-0007Y4-1p for guix-patches@gnu.org; Fri, 13 Oct 2023 11:57:37 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1697212651; x=1699027052; bh=RxNA6JOmerSy7Z0 YDmR3lOZRYkdDCUwl/h2L2ED6GQw=; b=iJXxwIkuR4GlaWUq3K3ZYLgvZxsKqCY dBJwdBRa//reWr89gxmLBsBWKN6b5/sGpOWTYPqo/v7ONWQ3dTgYDNM2CP3xAY3C ruJCjTaf2xAX31zh67wRPBfcOpadMA5gGysoQLNwRf8rH6IRf5Xq4IZ3r3Exs53g 16VhStT6Xrp0= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 0B9A5A0196 for ; Fri, 13 Oct 2023 17:57:31 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Fri, 13 Oct 2023 17:57:30 +0200 From: "Afkhami, Navid" Date: Fri, 13 Oct 2023 15:57:14 +0000 Message-ID: <78b0eabd77a637e8ce76f2ef7994dd88eddf063a.1697212635.git.Navid.Afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27934.000 X-TM-AS-Result: No-10--2.689800-5.000000 X-TMASE-MatchedRID: LFOyoH/XvLjgUbgLLPhW5hF4zyLyne+ATJDl9FKHbrkR0p2RbWIUIgbo TDS3zulAcjTcMkuJPYmDs24hteATnwYcH09cOokpqhcdnP91eXFh0Eb5uGGI1CBQRBOQhaJiJEb gebEoSmWslio5IdWDdNUf8/gZ0Wa4Q6dytbMjseXGL//8mlodAwK0ZgbTOeKU7rencS+jsJiUg5 UD6AlF0uO1cUsW4/41ElOOOz3JPpijxYyRBa/qJcFwgTvxipFa9xS3mVzWUuAojN1lLei7RXBJM oLu3c43gP+jIGHgZQYrd6qFivaZRTqosUTNlZuEfnsTtyiBaUcA4xJpJtBH/UmQ0Ih1xh6rsJVq d0/jmOtZb8OhxrCgBDVIWe9PfG2D9leimmhcnaXe4hkjgmJMlhA8jgfAt5oQ X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.689800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27934.000 X-TM-SNTS-SMTP: 3C97F6AA83BFC1D95518E1B9D17DCE93CD8C2BCF0BDC40017D5AEE65B7C5F3012000:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.mx.srv.dfn.de X-Spam_score_int: -42 X-Spam_score: -4.3 X-Spam_bar: ---- X-Spam_report: (-4.3 / 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, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, URIBL_SBL_A=0.1 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/statistics.scm (r-tgstat): Delete variable. --- gnu/packages/statistics.scm | 35 ----------------------------------- 1 file changed, 35 deletions(-) base-commit: dcfd4d9c4827ca6bfebeec46fe6bb8373c425a1c prerequisite-patch-id: 8b3f1b30e7ca1f6ddb21bf801faad91cce276dfd prerequisite-patch-id: 86f04eb38885c80e1fa302cec734581778e62c26 diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a21b47a9d3..7d6ec71e6f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -6525,41 +6525,6 @@ (define-public r-forcats manually \"recoding\").") (license license:gpl3))) -(define-public r-tgstat - (let ((changeset "4f8e60c03598f49aff6f5beeab40f2b995377e9f") - (revision "1")) - (package - (name "r-tgstat") - (version (string-append "1.0.2-" revision "." (string-take changeset 7))) - (source - (origin - (method hg-fetch) - (uri (hg-reference - (url "https://bitbucket.org/tanaylab/tgstat") - (changeset changeset))) - (file-name (string-append name "-" version "-checkout")) - (sha256 - (base32 - "0ilkkyximy77zbncm91kdfqbxf0qyndg16pd3q3p6a3xc9qcmxvn")))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-isnan - (lambda _ - (substitute* "src/tgstat.h" - (("#define isnan ::isnan") - "#define isnan std::isnan")) - #t))))) - (propagated-inputs - (list r-rcpp)) - (home-page "https://bitbucket.org/tanaylab/tgstat/") - (synopsis "Tanay's group statistical utilities") - (description - "The goal of tgstat is to provide fast and efficient statistical -tools.") - (license license:gpl2)))) - (define-public r-tgconfig (let ((commit "15cf199436ae0b2ac0006b2ca7f0aeeb5c9d4445") (revision "1")) From patchwork Fri Oct 13 15:57:15 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 54811 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id BC5D027BBEB; Fri, 13 Oct 2023 16:59:11 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 43D6927BBE2 for ; Fri, 13 Oct 2023 16:59:10 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qrKYj-0003jb-Dp; Fri, 13 Oct 2023 11:58:41 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qrKYi-0003j4-6z for guix-patches@gnu.org; Fri, 13 Oct 2023 11:58:40 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qrKYh-0007iW-Va for guix-patches@gnu.org; Fri, 13 Oct 2023 11:58:39 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qrKZ5-0007tp-08 for guix-patches@gnu.org; Fri, 13 Oct 2023 11:59:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66528] [PATCH 2/2] gnu: Add r-tgstat. Resent-From: "Afkhami, Navid" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 13 Oct 2023 15:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 66528 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 66528@debbugs.gnu.org Cc: "Afkhami, Navid" X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.169721269630215 (code B ref -1); Fri, 13 Oct 2023 15:59:02 +0000 Received: (at submit) by debbugs.gnu.org; 13 Oct 2023 15:58:16 +0000 Received: from localhost ([127.0.0.1]:47240 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qrKYK-0007rE-12 for submit@debbugs.gnu.org; Fri, 13 Oct 2023 11:58:16 -0400 Received: from lists.gnu.org ([2001:470:142::17]:35372) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qrKYF-0007qd-FO for submit@debbugs.gnu.org; Fri, 13 Oct 2023 11:58:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qrKXn-0003fj-4C for guix-patches@gnu.org; Fri, 13 Oct 2023 11:57:43 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qrKXl-0007Yg-Dj for guix-patches@gnu.org; Fri, 13 Oct 2023 11:57:42 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1697212657; x=1699027058; bh=eqpH2KQWEs8nB17mQSGqrKTVlO9pVihtLne87bKIAAc=; b=Q9HHYuGLcbAS RBPrSxW6y8tjOtFcX2yURfpnd+cl8KeeRJTDYAoPFVBwNA6YrD351kYJkccXv8wf fB8Mwd63NR9wPRr9do/1TEN14TUDqDLr2POFOWdBrHSqY2mUA1ePIHAMg9zCFOkI 8b09Oxct/6NBuwHM4Z1xT4cfyD0aLhk= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id BF86E160157 for ; Fri, 13 Oct 2023 17:57:37 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Fri, 13 Oct 2023 17:57:37 +0200 From: "Afkhami, Navid" Date: Fri, 13 Oct 2023 15:57:15 +0000 Message-ID: X-Mailer: git-send-email 2.34.1 In-Reply-To: <78b0eabd77a637e8ce76f2ef7994dd88eddf063a.1697212635.git.Navid.Afkhami@mdc-berlin.de> References: <78b0eabd77a637e8ce76f2ef7994dd88eddf063a.1697212635.git.Navid.Afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27934.000 X-TM-AS-Result: No-10-0.337400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEO5n zG+dPwIaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v/kwFzTzcgzhDGQt2RbsLmqvER UVOAFoxh7MSP7SLpuGI/h+VzXVDnD3Ot4hTskDRLdCok3ibXlQeuLFZZYlisfHxPMjOKY7A+u65 UDD0aDgsRB0bsfrpPI34T9cYMsdwxZ5LUFaJ6jmVs47Pth3Ab+i+EgGRdySQi1qxORHHBAK2HAF SwV1KC88vdDayQwL5Cqu75uQnVnLt1PALiA7B+s5kMsfZrjn3Rriwk488+qotqkGs/LBEZa8EFY CHVRuBROWg+GSIftMY4TDtwwKftL X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.337400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27934.000 X-TM-SNTS-SMTP: 4830BFD48A60F45D0F9E6343C9BDB09B60174AE2CE77F15BA1E0D3E2B75C51342000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-tgstat): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 1c37635ea5..de31f44dbd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -3257,6 +3257,29 @@ (define-public r-tgp noisy black-box functions.") (license license:lgpl2.0+))) +(define-public r-tgstat + (package + (name "r-tgstat") + (version "2.3.24") + (source + (origin + (method url-fetch) + (uri (cran-uri "tgstat" version)) + (sha256 + (base32 "0czd3j7z30jgb03813s0jc0701ypnwpkkq7var6n6f6cj7sdvc0l")))) + (properties `((upstream-name . "tgstat"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=tgstat") + (synopsis "Amos Tanay's Group High Performance Statistical Utilities") + (description + "This package provides a collection of high-performance utilities. +It can be used to compute distances, correlations, autocorrelations, +clustering, and other tasks. It also contains a graph clustering +algorithm described in MetaCell analysis of single-cell RNA-seq +data using K-nn graph partitions.") + (license license:gpl2))) + (define-public r-tidyft (package (name "r-tidyft")