From patchwork Fri Mar 3 13:07:15 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47569 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 DD80E16D2F; Fri, 3 Mar 2023 13:09:07 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,URIBL_BLOCKED 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 29FAA16D07 for ; Fri, 3 Mar 2023 13:09:07 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58s-0001Hq-2a; Fri, 03 Mar 2023 08:08:10 -0500 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 1pY58k-0001BY-Bg for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58k-0006kU-2n for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58j-0007dh-U9 for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 1/9] gnu: Add r-stringendo. References: <20230303125046.88428-1-navid.afkhami@mdc-berlin.de> In-Reply-To: <20230303125046.88428-1-navid.afkhami@mdc-berlin.de> Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784886129244 (code B ref 61933); Fri, 03 Mar 2023 13:08:01 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:41 +0000 Received: from localhost ([127.0.0.1]:59887 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58P-0007bb-GV for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:41 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:33689) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58M-0007bB-J4 for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:39 -0500 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=1677848851; x=1679663252; bh=e8/FECbnUtnR3fP O9u7eCWaSio1da7DUYPMKDlYPhec=; b=oYBAe6HXcx46vTFG1A67saMVZSMV9jR tekzxtk51z+8SmybUf339pL7wCu8l+JF0UM9Q7NKkwzkMAfwCbmo3Rzua6qFjMa0 Cs0QpwdXtKS5ZYOnx3FZGUuBN816uRZgrc1WC943wQJS9HbDsHNGKXpFNsbH3ITh qwasU705MVv0= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id C1DB3300333 for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:31 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:31 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:15 +0000 Message-ID: <20230303130723.88484-1-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-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--4.333000-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXR6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIHbkZ9nC3gWsvLn MD6cHrQV7MSP7SLpuGBq+GDzhZYNl0N7DjAdxZNTi8zVgXoAltsIJ+4gwXrEtwrbXMGDYqV+mZ3 96Gt5Hhdc7NRp3YI20MnuVnvXmps1xQk5Nw1683jVjQjH7+VWsP8qkGQ+pfp8xQ4/0Sg4tIUtSm nfkRkNzxkPoNI8CAvW4Yy52MhnSFMbG0bMSRYDWFhnoKW4f7Mf1c8RJIeS1QFmKmfpzNHMN X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.333000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: ADFEF9C48CD8E70263A7F526CE45D0A340701BE82C594A94D668743D4A76DD862002:F 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/bioinformatics.scm (r-stringendo): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) base-commit: 4f681cdbc27e6a922f24d4297efe3c0b823195f0 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 858fd1e975..caa50ce3bd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -793,6 +793,30 @@ (define-public r-rhtslib12 developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+)))) +(define-public r-stringendo + (let ((commit "83b8f2d82a09b33b9e895438bb523a021138be01") + (revision "1")) + (package + (name "r-stringendo") + (version (git-version "0.3.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/Stringendo") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ap0nhbyd6xx0yl2vgmwk38p22yrkv4k9hw13r35z4wf343rry6v")))) + (properties `((upstream-name . "Stringendo"))) + (build-system r-build-system) + (propagated-inputs (list r-devtools r-usethis)) + (home-page "https://github.com/vertesy/Stringendo") + (synopsis "Stringendo is a string parsing library") + (description + "String parsing functionalites for generating plotnames, filenames and path.") + (license license:gpl3)))) + (define-public r-streamgraph (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb") (revision "1")) From patchwork Fri Mar 3 13:07:16 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47563 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 B27B916D21; Fri, 3 Mar 2023 13:08:33 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 D677716D07 for ; Fri, 3 Mar 2023 13:08:31 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58m-0001CN-7v; Fri, 03 Mar 2023 08:08:04 -0500 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 1pY58k-0001Bf-PV for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58k-0006ke-H4 for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58k-0007dp-CV for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 2/9] gnu: Add r-readwriter. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784886229251 (code B ref 61933); Fri, 03 Mar 2023 13:08:02 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:42 +0000 Received: from localhost ([127.0.0.1]:59890 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58P-0007bd-Sn for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:42 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:43903) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58O-0007bE-DE for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:41 -0500 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=1677848853; x=1679663254; bh=cjlYL4vi+GHbEWYVgQzd7zPrOnoiX5tdubQw0VcsAmQ=; b=FRHJ+VbqmX83 KJOsldlGI5mgP3bN9SzUU9FXl6srDr12QdWRBfC9SaNf9u5tWuaptTf2q01ZKo4l LyeYQkgefUXI/4gkHmdSlYZ/llfFTHKbedIU2rdlYncJOg/Y+wXVJLKcg6OOTzsC N6UqJI282eFjrCKFMp4XDdQV5zv9or8= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id DDDBFA02C7 for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:33 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:33 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:16 +0000 Message-ID: <20230303130723.88484-2-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--2.707000-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VL6p xbTOjavyRLGO63kZy7gue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbednW9 y3u6VT2bA+OjLG1jwgD+goOl3Ilk0EQt7acrBPADdCok3ibXlQQseQVcTRnF2lwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYVKXc05A6WmsxWsZccKKYEuk0FNy3F3zF1Ht6slPc2RqEcJW PkLmWdOLM3WraZ10SgXHlyrxXnP6hiUNrJrkP8bO2G5BNG41OrX7GF+64huyLjmNKuuvgamoYI1 erIuEsW+g2RZj2FKy60Cnu9RmLpv X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.707000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: C7EBAC801D8BDFB3C1C58D16F8BA2733D5D7CA005B3037B86854F010835CAC2B2002:F 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/bioinformatics.scm (r-readwriter): New variable. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index caa50ce3bd..42e082765e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -817,6 +817,31 @@ (define-public r-stringendo "String parsing functionalites for generating plotnames, filenames and path.") (license license:gpl3)))) +(define-public r-readwriter + (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058") + (revision "1")) + (package + (name "r-readwriter") + (version (git-version "0.2.9" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/ReadWriter") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7")))) + (properties `((upstream-name . "ReadWriter"))) + (build-system r-build-system) + (propagated-inputs (list r-gdata r-gtools r-openxlsx r-readr + r-stringendo)) + (home-page "https://github.com/vertesy/ReadWriter") + (synopsis "Functions to read and write files conveniently") + (description + "ReadWriter is a set of R functions to read and write files conveniently.") + (license license:gpl3)))) + (define-public r-streamgraph (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb") (revision "1")) From patchwork Fri Mar 3 13:07:17 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47565 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 CEE0616D28; Fri, 3 Mar 2023 13:08:42 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,URIBL_BLOCKED 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 1E5A116D07 for ; Fri, 3 Mar 2023 13:08:42 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58n-0001Dw-VO; Fri, 03 Mar 2023 08:08:05 -0500 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 1pY58l-0001CM-TF for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58l-0006l6-Ks for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58l-0007eC-G4 for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 3/9] gnu: Add r-codeandroll2. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784886629305 (code B ref 61933); Fri, 03 Mar 2023 13:08:03 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:46 +0000 Received: from localhost ([127.0.0.1]:59900 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58U-0007cU-3c for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:46 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:52103) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58P-0007bG-EW for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:43 -0500 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=1677848855; x=1679663256; bh=/aOTl919MysA9QppW1aW18biY7qSvSyd1L5ZLxVIntw=; b=GO1y5bR9TZYD YMI7x4s7SNq822ApF91QuV0A/+u58hhDbXzVFLFkd/gvems4d4bsIiWqlf8rhhBV sb2WEOHSm1l7NKNWX+2jhLFKI0qsiu1hqzSpo7UDEQt0Dsmw6cpPUXZKPAx6XgDQ BHk5GNlULFMosVvNls5ApXayHlRN4Jo= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id F00B1160309 for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:34 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:34 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:17 +0000 Message-ID: <20230303130723.88484-3-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--3.954400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXMx8ROcn611jkpOkDFSV28wIdG4n3A2CkfOaYwP8dcX5IvK4LrXs1aSdEcnIP1FQIY2i R7K8WcsxwyxC8d/tsmz3mnWKOM3JFMnOeBW4TJ/fdCok3ibXlQeuLFZZYlisfHxPMjOKY7A9qHX ONfTwSQsRB0bsfrpPI34T9cYMsdwxJuJQGiNJgSNjd26haE+ZPqhy5k6LrnT7gmcrsdMuW2l/Fe 0uAy69TYHdY76uz++YsNGMdNMV/jbfvNSGxReey9j9jkK1UOLtriwk488+qotqkGs/LBEZa8EFY CHVRuBROWg+GSIftMY4TDtwwKftL X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.954400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: 6C8B502133BE3A6E7013DC10CCF50AE4231D9281E853FAD53D5FFFF4792E6D622002:F 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/bioinformatics.scm (r-codeandroll2): New variable. --- gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 42e082765e..fdfbf6459b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -719,6 +719,40 @@ (define-public r-btools for all types of microbial diversity analyses.") (license license:expat)))) +(define-public r-codeandroll2 + (let ((commit "d58e258851a5c0b430e8620d34dbeefb597c548f") + (revision "1")) + (package + (name "r-codeandroll2") + (version (git-version "2.3.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/CodeAndRoll2") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sy88mfgw6qqhpnlc5020qzr1jllkcrxfhl2lw42bkl5nb56is71")))) + (properties `((upstream-name . "CodeAndRoll2"))) + (build-system r-build-system) + (propagated-inputs (list r-colorramps + r-dplyr + r-gplots + r-gtools + r-plyr + r-rcolorbrewer + r-sessioninfo + r-sm + r-stringendo + r-stringr)) + (home-page "https://github.com/vertesy/CodeAndRoll2") + (synopsis "CodeAndRoll2 for vector, matrix and list manipulations") + (description + "CodeAndRoll2 is a set of more than 130 productivity functions. +These functions are used by MarkdownReports, ggExpress, SeuratUtils.") + (license license:gpl3)))) + (define-public r-conospanel (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9") (revision "1")) From patchwork Fri Mar 3 13:07:18 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47571 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 A41F716D28; Fri, 3 Mar 2023 13:09:12 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,URIBL_BLOCKED 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 EE07C16D07 for ; Fri, 3 Mar 2023 13:09:11 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58s-0001I8-Fc; Fri, 03 Mar 2023 08:08:10 -0500 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 1pY58l-0001Bu-4L for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58k-0006kl-SM for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58k-0007dw-Ng for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 4/9] gnu: Add r-markdownhelpers. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784886429283 (code B ref 61933); Fri, 03 Mar 2023 13:08:02 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:44 +0000 Received: from localhost ([127.0.0.1]:59894 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58S-0007c9-5h for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:44 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:53049) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58P-0007bI-VE for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:42 -0500 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=1677848855; x=1679663256; bh=e2sScRW7/SbUxqbGU7CpXX7PY3xiwTySFEEmdQUSB7Y=; b=SJdi1IiboFZ6 vrtDymVxYR3xNDwryL9pgCy3IHypypQ43R97SiVEe70mAHOfsWBsLp6nUSG/jpXY jaB1MkG5PyzT1w5cvQK1FkUC3gea0aIPdh4NcwT4kzICu1GYNFIsTbp8y38zZ76O /Cjfp+cHJ9yWrKWHwtNIjQ2OLre66Bg= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id E26D016030D for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:35 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:35 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:18 +0000 Message-ID: <20230303130723.88484-4-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--3.570700-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXR6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIEJ1hMCC63pY2Lg EVfggSlj4l88hSeZMb0gljz7CRMbZ0N7DjAdxZNTi8zVgXoAltsIJ+4gwXrEtwrbXMGDYqV+qsz jolCcvyDs7DdCwYm5RGpXQOEwtnm6eGG/viazvWAvkVrZhO9lDfoiMmmmz1qUq6J+jOBVgHnWoD OlTejBMfNooEZbbAGPwHcHzUiqKl8bG0bMSRYDWFhnoKW4f7Mf1c8RJIeS1QFmKmfpzNHMN X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.570700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: 278FC840995875EF3A5FDD69696946FCA0BAB779C9E5B100A40BCDAA221AF7B92002:F 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/bioinformatics.scm (r-markdownhelpers): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fdfbf6459b..c6c0da74ff 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8813,6 +8813,30 @@ (define-public r-sccustomize visualization and analysis of single-cell data using R.") (license license:gpl3+)))) +(define-public r-markdownhelpers + (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe") + (revision "1")) + (package + (name "r-markdownhelpers") + (version (git-version "0.2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/MarkdownHelpers") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1d18s2ydhfjm3hjkxz42dirhwrrv792m6mvkmypallaa2qnwrmkg")))) + (properties `((upstream-name . "MarkdownHelpers"))) + (build-system r-build-system) + (propagated-inputs (list r-devtools r-stringendo r-usethis)) + (home-page "https://github.com/vertesy/MarkdownHelpers") + (synopsis "Helper functions for MarkdownReports and ggExpress") + (description + "Set of R functions to parse markdown and other generic helpers.") + (license license:gpl3)))) + (define-public r-snapatac (package (name "r-snapatac") From patchwork Fri Mar 3 13:07:19 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47568 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 689E816D21; Fri, 3 Mar 2023 13:09:06 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 69BF916D07 for ; Fri, 3 Mar 2023 13:09:04 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58q-0001Fk-1Q; Fri, 03 Mar 2023 08:08:08 -0500 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 1pY58l-0001CA-Gw for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58l-0006kx-6t for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58l-0007e3-2e for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 5/9] gnu: Add r-markdownreports. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784886629297 (code B ref 61933); Fri, 03 Mar 2023 13:08:03 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:46 +0000 Received: from localhost ([127.0.0.1]:59898 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58T-0007cN-LZ for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:46 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:47735) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58R-0007bK-4Y for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:43 -0500 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=1677848856; x=1679663257; bh=PO9a8DUz6hIMr3K29B3OWi6/Ukqu+zCCml3ZrUbQeyE=; b=L7/SxRW9g5C4 G4ypI2B4ZeVyLcjGj8u8cnNfCFMD5c+9xjBQMGjS2SRVrhRn83vwfSHbFOnYxTqr bT/h7wdKa26Ybn5A0Q4zTXbdBbuciKWE1LbiS4oECTp5S+CbergW1tG+qz+iEMsg xPd4X/Z7qgk2b2n71iQGihMXRgS4Ukc= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id DE9B8300346 for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:36 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:36 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:19 +0000 Message-ID: <20230303130723.88484-5-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--3.281700-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VCzy bVqWyY2N+JfPIUnmTG/K4w30FlubyQIdG4n3A2CkfOaYwP8dcX5IvK4LrXs1aSdEcnIP1FQIY2i R7K8WcszWhKYfDziAdPJrrM6i6Ao7Bw746+zsRpDdCok3ibXlQeuLFZZYlisfHxPMjOKY7A8Lbi gRnpKlKTpcQTtiHDgWrEZ/07vi8w0iCogUjPmCsKZUkAT5yyFqwsi0wMl8HQzvO/kmc1hOmZ9AK 8brBUyJxtSOLDGeHyzXYedS7FIioKSzNYAWu9nwt0oQIuj+SVeFEVfQxs3N6ZDgmt8QekvB5maC eNv/LIzVGQdqwsDiEg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.281700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: FF40AE3D58DD853E73C1ED9F10852D2A7114DC70BF3D99D44114EF5B83CC028D2002:F 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/bioinformatics.scm (r-markdownreports): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6c0da74ff..b311ec6c33 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8837,6 +8837,43 @@ (define-public r-markdownhelpers "Set of R functions to parse markdown and other generic helpers.") (license license:gpl3)))) +(define-public r-markdownreports + (let ((commit "3ba1103e3ddc6df3a0c090eb884f5e65c461eb31") + (revision "1")) + (package + (name "r-markdownreports") + (version (git-version "4.5.9" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/MarkdownReports") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1xmasdb630b6nvxi5m1i8pyxiy49nxpzyxf9h8spdppx92rhdkc8")))) + (properties `((upstream-name . "MarkdownReports"))) + (build-system r-build-system) + (propagated-inputs (list r-clipr + r-codeandroll2 + r-colorramps + r-devtools + r-gplots + r-markdownhelpers + r-rcolorbrewer + r-readwriter + r-sessioninfo + r-sm + r-stringendo + r-venndiagram + r-vioplot)) + (home-page "https://github.com/vertesy/MarkdownReports") + (synopsis "Tool for generating cientific figures and reports") + (description + "This is a set of R functions that allows you to generate precise figures. +This tool will create clean markdown reports about what you just discovered.") + (license license:gpl3)))) + (define-public r-snapatac (package (name "r-snapatac") From patchwork Fri Mar 3 13:07:20 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47570 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 5BABF16D21; Fri, 3 Mar 2023 13:09:09 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 2CC0016D1F for ; Fri, 3 Mar 2023 13:09:07 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58q-0001GM-AT; Fri, 03 Mar 2023 08:08:08 -0500 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 1pY58m-0001CU-B1 for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58m-0006lC-2j for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58l-0007eJ-Uv for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 6/9] gnu: Add r-ggexpress. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784886629311 (code B ref 61933); Fri, 03 Mar 2023 13:08:03 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:46 +0000 Received: from localhost ([127.0.0.1]:59902 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58U-0007cb-FL for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:46 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:37795) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58S-0007bN-4z for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:44 -0500 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=1677848857; x=1679663258; bh=LFBrLxz02b5AxLFB+ZtkY/v2ebXtcdexIZZknQKjeUA=; b=ProMa6HfHV0k 9xcqLSehWNOVNyKdxkuVWVM9Q3lbxG8VHNt6zUwquR6zjK4NqHFX/+PsZt/t/auh x/40L+VjS9pVbDS2Grxe0Cz5ug+DxBqSof2n5dHkAI3P1UDVIgE0edrlSr2W3lyS YHMGZfLBXdv9YAiswEnuMYtyu603bSI= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id C8EBB30034E for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:37 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:37 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:20 +0000 Message-ID: <20230303130723.88484-6-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--2.134200-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiJ6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFDLy10jRvW6qQue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbed7Sc dpy2ZKwKGctMEqTuN+rSIRR31JzPS27YWB4baXJJvwVJGkXUdCaVjgXyvS9c/Z42Lekd+hLkjL8 WDWZGeoqEbr6VH4TuZmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5dl8TNqkmhnNjhB+ XA20GV1qbTpLIqZdxN3J/sTLfOeob87ibF3A0IVtnJBdVCYm6dubTrypg7VmbKqVLhqlFopNzfU ipEs8Mbox9rqorLqIj47jot1RqlnCuhB+Hs2Q+XFRuRzIFoKqH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.134200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: F8E56468D5DE4A5FFCE99B03D490CFF8F807E48D7EC7720A6B229DB5E7E0CA942002:F 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/bioinformatics.scm (r-ggexpress): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b311ec6c33..14efaa9570 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8302,6 +8302,43 @@ (define-public infernal (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-ggexpress + (let ((commit "82f169385f87af328ff971195c2f64ff3c573a8a") + (revision "1")) + (package + (name "r-ggexpress") + (version (git-version "0.6.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/ggExpress") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "122hnw8xv33ngcd4fd7hmf817a06ih1knrxxi0cgklj1fwinm0z4")))) + (properties `((upstream-name . "ggExpress"))) + (build-system r-build-system) + (propagated-inputs (list r-cowplot + r-ggplot2 + r-ggpubr + r-markdownhelpers + r-markdownreports + r-rcolorbrewer + r-sessioninfo + r-seurat + r-sm + r-stringendo + r-tidyverse)) + (home-page "https://github.com/vertesy/ggExpress") + (synopsis + "This is a fast tool to create, annotate and export plots in R") + (description + "This package is a set of R functions for generating precise figures. +This tool helps you to create clean markdown reports about what you just +discovered with your analysis script.") + (license license:gpl3)))) + (define-public r-gg3d (let ((commit "ffdd837d30c1671cd0895db94bdd7b1594dbfcb0") (revision "1")) From patchwork Fri Mar 3 13:07:21 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47567 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 1247116D28; Fri, 3 Mar 2023 13:08:54 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,URIBL_BLOCKED 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 825E316D1F for ; Fri, 3 Mar 2023 13:08:53 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58n-0001DF-GS; Fri, 03 Mar 2023 08:08:05 -0500 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 1pY58m-0001Ci-N6 for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58m-0006lK-Ed for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58m-0007eQ-AN for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 7/9] gnu: Add r-tictoc. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784887029332 (code B ref 61933); Fri, 03 Mar 2023 13:08:04 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:50 +0000 Received: from localhost ([127.0.0.1]:59906 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58X-0007d1-ST for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:50 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:56027) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58T-0007bU-8Y for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:45 -0500 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=1677848858; x=1679663259; bh=bDroPSswHC5FI4CkdUWkUlt8J0nEp8J4UDyTz32pDiw=; b=JyLCvLR9uhOh OUKolHCel4SiKQ7kOwTh5RUK2/uX6VbSkaZb2dabSYr8fABXkHuBMeoUZr9Wt8ja f8sfXP20D/m7YZ52oYaOs8PrWaZjFOehpZzpxXzA+59//xpJnvYrgwB2YfHavXmk /gaNN80TfhbgkzNx5R2R1iQ7PJt6KaM= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id C7B35300354 for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:38 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:38 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:21 +0000 Message-ID: <20230303130723.88484-7-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--5.450000-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8t81T+vai/Z6Y5ZGw7wyeHY87 NwWBxSviv9PXEePqxlUxDwYhMY4MtJIp5MhAnVvNQsahOMIZ15T5//buCv56OlwV2iaAfSWcURS Scn+QSXmVV1G+Ck2l7+gtHj7OwNO2BSJy8ngwKGZTERcHhJL+KeJcxpkIvzahsgd7QHebgFr33a fqIDpacEsXneEly+yc= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.450000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: 83EC0E4FF847F9A85AF1CF19BD41D400D2CEE1DB81AD4002F46F221486741B3B2002:F 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/bioinformatics.scm (r-tictoc): New variable. --- gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 14efaa9570..42d0923ab1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8960,6 +8960,28 @@ (define-public r-snapatac single cell ATAC-seq sequencing data.") (license license:gpl3))) +(define-public r-tictoc + (package + (name "r-tictoc") + (version "1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "tictoc" version)) + (sha256 + (base32 + "0ka7zd857xfqb5afn0psn0yzfv2qjb0ddxfyiq6aggbnla5qc3qj")))) + (properties `((upstream-name . "tictoc"))) + (build-system r-build-system) + (home-page "https://github.com/jabiru/tictoc") + (synopsis + "Functions for timing R scripts and implementations of stack and list structures") + (description + "The tictoc package provides the timing functions tic and toc that can be nested. +It provides an alternative to @code{system.time()} with a different syntax similar to +that in another well-known software package. tic and toc are easy to use, and are +especially useful when timing several sections in more than a few lines of code.") + (license license:asl2.0))) + (define-public r-tsis (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc") (revision "1")) From patchwork Fri Mar 3 13:07:22 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47566 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 7170616D21; Fri, 3 Mar 2023 13:08:48 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 B9F0A16D07 for ; Fri, 3 Mar 2023 13:08:46 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58r-0001Hc-J9; Fri, 03 Mar 2023 08:08:09 -0500 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 1pY58n-0001D5-3l for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:05 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58m-0006lT-RR for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58m-0007eY-NZ for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 8/9] gnu: Add r-hgnchelper. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784887029338 (code B ref 61933); Fri, 03 Mar 2023 13:08:04 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:50 +0000 Received: from localhost ([127.0.0.1]:59908 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58Y-0007d3-6O for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:50 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:34225) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58V-0007bs-RJ for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:48 -0500 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=1677848861; x=1679663262; bh=BpzSj+FPvrnGXs8XXvo+kIFcxHLmsqDH3eqFSuV0c2c=; b=S0JnnbjgQh8q 6UAZ0TwJ+Bxt674eHaPGsKn7HYXZBSll08J7hSDlfeaFqiHV+uAyXxLodRsWfQXx h+/nM4E/krZugIo1g6iZauKu+XYuvjZXsItufNXdKvnzdamjJJapwXoCQs9t/R3Z ITDK/uFGzuVmV628hNZQg5TStb/on6s= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 829DAA02C7 for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:41 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:41 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:22 +0000 Message-ID: <20230303130723.88484-8-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--4.401400-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfN6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VKcl vg4wawq3/YUtGtrcVxDuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHzsW XSKAZ9lSoWqIUGqis8lyL1R5BZDlEZ28ZQS4q9JyC+Y2uxPjocir/AahqlbtXlCkt7JatNPWeAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DHn6zxxjdwFU+tsUOkhussQfUz9FhIrH23HM7 zH2Hcvp3lXjFlrScSEM6hL5GbVhlQhDPqUsHKdLdrfd0GstA/KBF9POVxFJE2uLCTjzz6qi2qQa z8sERlrwQVgIdVG4FE5aD4ZIh+0xjhMO3DAp+0s= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.401400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: 77D8B996090DA377FB719E54CA5B5929740DDDC6F3B6AF811C0B22A6303587572002:F 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/bioinformatics.scm (r-hgnchelper): New variable. --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 42d0923ab1..b179fcb61a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9139,6 +9139,29 @@ (define-public r-archr "This package is designed to streamline scATAC analyses in R.") (license license:gpl2+)))) +(define-public r-hgnchelper + (package + (name "r-hgnchelper") + (version "0.8.1") + (source (origin + (method url-fetch) + (uri (cran-uri "HGNChelper" version)) + (sha256 + (base32 + "0qwkk5658j4j6w2wgvxkp38cyvscjp93d3zc7gb97vcihqx0ngxa")))) + (properties `((upstream-name . "HGNChelper"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/waldronlab/HGNChelper") + (synopsis + "Identification and correction of invalid gene symbols for human and mouse") + (description + "Set of R functions for identifying and correcting HGNC human gene symbols. +In addition, you can identify MGI mouse gene symbols, which have been converted +to date format by Excel, withdrawn, or aliased. Also contains functions for +reversibly converting between HGNC symbols and valid R names.") + (license license:gpl2+))) + (define-public r-icellnet ;; v1.0 tagged in 2020, last commit contains many fixes. ;; DESCRIPTION says Version: 0.0.0.9000. From patchwork Fri Mar 3 13:07:23 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 47564 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 9B17416D21; Fri, 3 Mar 2023 13:08:40 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.8 required=5.0 tests=DKIM_INVALID,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 76EB716D07 for ; Fri, 3 Mar 2023 13:08:38 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pY58o-0001F4-PE; Fri, 03 Mar 2023 08:08:06 -0500 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 1pY58n-0001DH-Hn for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:05 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pY58n-0006lY-97 for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pY58n-0007ef-3Z for guix-patches@gnu.org; Fri, 03 Mar 2023 08:08:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61933] [PATCH vREVISION 9/9] gnu: Add r-seurat-utils. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 03 Mar 2023 13:08:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 61933 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <61933@debbugs.gnu.org> Cc: Navid Afkhami Received: via spool by 61933-submit@debbugs.gnu.org id=B61933.167784887229348 (code B ref 61933); Fri, 03 Mar 2023 13:08:05 +0000 Received: (at 61933) by debbugs.gnu.org; 3 Mar 2023 13:07:52 +0000 Received: from localhost ([127.0.0.1]:59910 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58Z-0007dH-IO for submit@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:52 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:36693) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pY58X-0007c3-04 for 61933@debbugs.gnu.org; Fri, 03 Mar 2023 08:07:49 -0500 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=1677848862; x=1679663263; bh=LWv0LNBu/4SiK7xdlJcb+CwKcwzaeKqQmqqR4MQW/xs=; b=H8YIoZpqtyoR NpRUxtqUVNGEj+yJTHLb0cRHCQLOE8XE1SX7kRTITrs73yO2d/4pAQvF2bSU//dK 0jQqtME6QjXhxLh7p366rBScjS2NXhrftUqo3RiLpkARQ0IaT6I8IlgIG3m03Mk4 AFBI9dU6Ux04Gw0zBhtmlD25U0hHZ34= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id A7A7A16030D for <61933@debbugs.gnu.org>; Fri, 3 Mar 2023 14:07:42 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.21; Fri, 3 Mar 2023 14:07:42 +0100 From: Navid Afkhami Date: Fri, 3 Mar 2023 13:07:23 +0000 Message-ID: <20230303130723.88484-9-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> References: <20230303130723.88484-1-navid.afkhami@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-AS-Result: No-10--3.221700-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiJ6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VNnf JrUSEbFDohg0wXRQu+0ue6riVYm/hx1hN+DNBjvOa87CDXaKRVILwteD+QnyUBHfiujuTbedh29 vQ0dGf2NwyxC8d/tsm4viftuapucu9GvnaLY1JSzGq2xUjwqsmk+crEA4+nhZrYTBYmxQ48yUg5 UD6AlF0sX4oKkYTfsImyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5dz6BaVES2VAw5yK y4qBrEvnyG+3lBEYMSgvTRnnW+leNbA4wMaICeskv702D4cIIwRRzZJwkn9I0VDfYNmFPMc2igV 6YVW1erox9rqorLqIj47jot1RqlnCuhB+Hs2Q+XFRuRzIFoKqH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.221700-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27480.007 X-TM-SNTS-SMTP: C0E6AA6AF7D6EF31CDC6AD626E45466015AA887D31122227653BE835FADFF5942002:F 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/bioinformatics.scm (r-seurat-utils): New variable. --- gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b179fcb61a..31dd2d856f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15955,6 +15955,61 @@ (define-public r-scopeloomr files.") (license license:expat)))) +(define-public r-seurat-utils + (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5") + (revision "1")) + (package + (name "r-seurat-utils") + (version (git-version "1.6.5" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/Seurat.utils") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762")))) + (properties `((upstream-name . "Seurat.utils"))) + (build-system r-build-system) + (propagated-inputs (list r-codeandroll2 + r-cowplot + r-dplyr + r-ggcorrplot + r-ggexpress + r-ggplot2 + r-ggpubr + r-ggrepel + r-hgnchelper + r-htmlwidgets + r-markdownhelpers + r-markdownreports + r-matrix + r-matrixstats + r-princurve + r-r-utils + r-readr + r-readwriter + r-reshape2 + r-scales + r-seurat + r-soupx + r-sparsematrixstats + r-stringendo + r-stringr + r-tibble + r-tictoc + r-vroom)) + (home-page "https://github.com/vertesy/Seurat.utils") + (synopsis "Seurat.utils is a collection of utility functions for Seurat") + (description + "This is a collection of utility functions for Seurat v3. +These Functions allow the automation and multiplexing of plotting, +3D plotting, visualisation of statistics & QC, interaction with the +Seurat object. Some functionalities require functions from +CodeAndRoll and MarkdownReports libraries.") + (license license:gpl3)))) + (define-public r-seuratwrappers ;; There are no releases or tags. (let ((commit "d28512f804d5fe05e6d68900ca9221020d52cf1d")