From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:25:28 2023 Received: (at submit) by debbugs.gnu.org; 27 Feb 2023 10:25:28 +0000 Received: from localhost ([127.0.0.1]:46093 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWahE-0001Kw-6n for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:25:28 -0500 Received: from lists.gnu.org ([209.51.188.17]:41880) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWahB-0001Kf-G4 for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:25:26 -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 1pWagy-0005AN-Pg for guix-patches@gnu.org; Mon, 27 Feb 2023 05:25:14 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pWagw-0005Zc-Co for guix-patches@gnu.org; Mon, 27 Feb 2023 05:25:12 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= mime-version:content-type:content-type:content-language :accept-language:message-id:date:date:subject:subject:from:from :received:received; s=mdc; t=1677493497; x=1679307898; bh=hhK2v/ 1xTz57C+zwP4o6pnzMTAIL7XXLqs8ZE4XmB/Y=; b=MumbFy8SOKSMIM0wRsYVEK TgmrHvyTyTVdIZvi++LDukLbUzDK5Xie80TxJBSJaOlBPV4LRjJ7VM7EG5GyPZnD IlJX7munyhkn+WuOwqU/AeBoAr9zOuPvJgNeJ1rnfor9/xC4wyB9h4f4Iwf6dbEn 6r67FPTsPHHbhJUOCsHQA= 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 86117300131 for ; Mon, 27 Feb 2023 11:24:57 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) 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; Mon, 27 Feb 2023 11:24:56 +0100 Received: from SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a]) by SW-IT-P-EX4.mdc-berlin.net ([fe80::e55f:895f:3b41:ec6a%2]) with mapi id 15.01.2507.021; Mon, 27 Feb 2023 11:24:56 +0100 From: "MadalinIonel.Patrascu@mdc-berlin.de" To: "guix-patches@gnu.org" Subject: [PAtCH] gnu: Add r-simplermarkdown, r-rcppspdlog, r-n2r, r-sccore, r-leidenalg, r-drat, r-dendsort, r-pagoda2, r-conospanel, r-p2data, r-pma, r-rmumps and r-conos. Thread-Topic: [PAtCH] gnu: Add r-simplermarkdown, r-rcppspdlog, r-n2r, r-sccore, r-leidenalg, r-drat, r-dendsort, r-pagoda2, r-conospanel, r-p2data, r-pma, r-rmumps and r-conos. Thread-Index: AQHZSpWphh72lm5o70GijE7dwoU0Ng== Date: Mon, 27 Feb 2023 10:24:56 +0000 Message-ID: <669c9a4b05f74824b87f3bb57fd23c98@mdc-berlin.de> Accept-Language: en-US, de-DE Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [141.80.113.51] x-tm-as-product-ver: SMEX-14.0.0.3092-9.0.1002-27472.006 x-tm-as-result: No-10--8.884600-5.000000 x-tmase-matchedrid: n8dyCgqCzuufkHSWeTTytMG0UNgaZpYqGsvgUMYAn4UWzPTbxO7R+tIS YzBUt2RaXVsEWVqYqaivJcrLMYkA70UuXkWTSi/R30kDaWZBE1RU4sxFq6igEUqa6TyhyXvPW4Z nuvI7TMq4be8l1U58znq+qg096V499cF/7GxXM9Y1zTm7Qr1KLbcLzBNuJmVOqU5CNByvM6V9Q+ 0wSn65+4A+zZbAFdrSgYDt2kRukG0sm617PZ0pZ+LzNWBegCW27ff0Y3IpHxrAeVm1nnWZdADJm NK5f3bTcXPZHI11f7pi7fhcJOOC2dtsxSWNXoQEC4thAUNx+ok= x-tm-as-user-approved-sender: Yes x-tm-as-user-blocked-sender: No x-tmase-result: 10--8.884600-5.000000 x-tmase-version: SMEX-14.0.0.3092-9.0.1002-27472.006 x-tm-snts-smtp: CA4444225876E8BCAA75C4E99EFD2C92765D007A96171286350D030450F17D372002:F Content-Type: multipart/alternative; boundary="_000_669c9a4b05f74824b87f3bb57fd23c98mdcberlinde_" MIME-Version: 1.0 Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.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, HTML_MESSAGE=0.001, 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-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit 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: -2.4 (--) --_000_669c9a4b05f74824b87f3bb57fd23c98mdcberlinde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable * * gnu/packages/cran.scm (r-simplermarkdown, r-rcppspdlog, r-n2r, r-sc= core, r-leidenalg, r-drat, r-dendsort, r-pagoda2, r-conospanel, r-p2data, r= -pma, r-rmumps): New variables. * * gnu/packages/bioconductor.scm (r-conos): New variable. --_000_669c9a4b05f74824b87f3bb57fd23c98mdcberlinde_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

  • * gnu/packages/cran.scm (r-simplermarkdown, r-rcppspdlog,&nb= sp;r-n2r, r-sccore, r-leidenalg, r-d= rat, r-dendsort, r-pagoda2, r-conospanel, r-p2data, r-pma, r-rmumps): New variables.
  • * gnu/packages/bioconductor.scm (r-con= os): New variable.

--_000_669c9a4b05f74824b87f3bb57fd23c98mdcberlinde_-- From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:12 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:12 +0000 Received: from localhost ([127.0.0.1]:46101 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakp-0001Qo-SW for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:12 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:57909) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWako-0001QK-4Y for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:10 -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=1677493743; x=1679308144; bh=+4VQSmDmJytRlgb SK9ID36CQ2wEOhXrTdt5k3zgIPNY=; b=KlKlINnGrt7QBVKFWMKXMmumvNKoI+Q ZnYrkwIJ4MtWoe8hIfe7MeBql5plquqNJMhTuGbid8Fo4yA3hTjXg1Jb3/YxoP4U a0BPgU7es5DL/y0glw4apcG1vc1vuJeYz4tnVPQV/0VjGa9B35LiyQgsnt/43YLp aS7STh55n43Q= 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 82B04160123 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:03 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:00 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 01/13] gnu: Add r-simplermarkdown. Date: Mon, 27 Feb 2023 11:28:38 +0100 Message-ID: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--7.317600-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6GFMYlDUzwr0XjfR3d0weRh7W0X9FnZcMeA9 iB1Lee2SGsZX0q3FpiOhAZQXEXXZuqOJ+h+s5fKarm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu92KvEVWmYr1qULJ6yyh20lz0m1eU2mBKmrRfoMnKlyiYfGjBoWP0C0KfPgsLBaFaA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.317600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 5F0EAB2976B78B6D045B29FEA66021500D76CF2CBD041F520855D4837E2E67602002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-simplermarkdown): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c80e98134a..f63112c3be 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9652,6 +9652,28 @@ (define-public r-signal It also includes interpolation functions.") (license license:gpl2))) +(define-public r-simplermarkdown + (package + (name "r-simplermarkdown") + (version "0.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "simplermarkdown" version)) + (sha256 + (base32 "069pgx5m22rdqa21lyn5zqm9ym3g7w6z1d2wjwms8b1f2cp6266g")))) + (properties `((upstream-name . "simplermarkdown"))) + (build-system r-build-system) + (propagated-inputs (list r-rjson)) + (home-page "https://github.com/djvanderlaan/simplermarkdown") + (synopsis "Simple engine for generating reports using R") + (description + "This package runs R-code present in a pandoc markdown file and includes the +resulting output in the resulting markdown file. This file can then be converted +into any of the output formats supported by pandoc. The package can also be used +as an engine for writing package vignettes.") + (license license:gpl3+))) + (define-public r-gsubfn (package (name "r-gsubfn") base-commit: 5d10644371abd54d0edcd638691113f0a92de743 -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:17 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:17 +0000 Received: from localhost ([127.0.0.1]:46106 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWaku-0001RG-91 for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:17 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47821) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakn-0001QI-OW for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:10 -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=1677493742; x=1679308143; bh=g2CEWIR8yJnhZUl/q7kkqWTa5Rr+c8dFSVBf/72RreA=; b=Oe1q1LW2LFC+ XEgJaA8LrEfmZYItshCCfFvct+Jyl5Idk/7iExVitGfqMhmc99M0Fsy90L4+7Wod KnTkT4jqRWajMuIninC2YVwW1udi6HEjv59v6x5B7fdswV0YXmJP/JKbpG1GdrGu Fko7i0PneWT5UOvtu/N/3KO0Q383Jbo= 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 99FA216011B for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:01 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 02/13] gnu: Add r-rcppspdlog. Date: Mon, 27 Feb 2023 11:28:39 +0100 Message-ID: <20230227102850.18782-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--5.656400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6dXu122+iJtrWN3XQ/7wsT6s1VKAXn4vh2Lg EVfggSliR1PJRLXDzQe03npH1yTi1h3Oo6YoUrdbdCok3ibXlQeuLFZZYlisfHxPMjOKY7A+u65 UDD0aDgsRB0bsfrpPIXzYxeQR1DvsGT2h+gGH6EeRQgfoy3PhxHxz319UyuAYKXn75vU6Njuyk4 nnWoH35 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.656400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: C85EE0AE63821093B4AF493EE5BEBEC85018F126943782501D17F48E8218DF982002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-rcppspdlog): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f63112c3be..46b8dbc9ec 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4992,6 +4992,30 @@ (define-public r-rcppml factorization and divisive clustering for large sparse and dense matrices.") (license license:gpl2+))) +(define-public r-rcppspdlog + (package + (name "r-rcppspdlog") + (version "0.0.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppSpdlog" version)) + (sha256 + (base32 "1nan0hm49xdl2l1lskm1jf01clfh7aw2v6h57j35qysvg8219fcx")))) + (properties `((upstream-name . "RcppSpdlog"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (native-inputs (list r-simplermarkdown)) + (home-page "https://github.com/eddelbuettel/rcppspdlog") + (synopsis "R and C++ interfaces to 'spdlog' C++ header library for logging") + (description + "The spdlog library is a widely-used and very capable header-only C++ library +for logging. This package includes its headers as an R package to permit other R +packages to deploy it via a simple @code{LinkingTo: RcppSpdlog}. As of version +0.0.9, it also provides both simple R logging functions and compiled functions +callable by other packages.") + (license license:gpl2+))) + (define-public r-rcppthread (package (name "r-rcppthread") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:17 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:17 +0000 Received: from localhost ([127.0.0.1]:46109 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakv-0001RV-4f for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:17 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:46741) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWako-0001QM-RZ for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:11 -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=1677493744; x=1679308145; bh=pdGZP7oIpkRbDj1ZMyK+XXpeyTl2az2d/wbekbg3miY=; b=ic5OA3vgS4zC 9SH3ojjliiaIDReuDB+LJpkfalS6Aps5sgnK1ckGp7g95gs4HQ48oMy9S2M9TgKv upk/r8QXdeCdwVwyJrxGPydf+HgbE066+EbN/e0JNw6qQ4P69OWo1VYMyFBkhwcf YZKXsEtRaXhgHqRTTGfflTWybsaAwV0= 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 BFCC816014E for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:04 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 03/13] gnu: Add r-n2r. Date: Mon, 27 Feb 2023 11:28:40 +0100 Message-ID: <20230227102850.18782-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10-1.719400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6L2JUO7sQ9/yCMN25048EeqY5ZGw7wyeHNZ6 ZIsdh38qjQfznAHGNCFaqBFpUBa9V0N7DjAdxZNTi8zVgXoAltuJ5hXsnxp7jC24oEZ6SpSk6XE E7Yhw4FomRy0XNgU9HzUNOfcVPXVriB9EDrRKq58NarKsMxzy0kgBpBbwEirVAZTWiSfgxfXNoU to89wycg5N+bsuxLfIWhuHBSve6ht8iatREjfpDE8nb9DwdQ4C2jbSab1pg0UjxFpwn53SOfhj5 CZkmSyI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.719400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 167AF0EA3CB291F954EF2FC6F781DB61ED79F159C955C904D398BC7CEA9FC42B2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-n2r): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 46b8dbc9ec..184cbd6d7f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8334,6 +8334,32 @@ (define-public r-tinytest ") (license license:gpl3))) +(define-public r-n2r + (package + (name "r-n2r") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "N2R" version)) + (sha256 + (base32 "12bv7xx6j6222qgpv6g61i68017fz0x6fjg9a9k5yhgw3zk05hpk")))) + (properties `((upstream-name . "N2R"))) + (build-system r-build-system) + (propagated-inputs + (list r-matrix + r-rcpp + r-rcppeigen + r-rcppspdlog)) + (home-page "https://github.com/kharchenkolab/N2R") + (synopsis "Fast and scalable approximate k-Nearest Neighbor search methods") + (description + "This package implements methods to perform fast approximate K-nearest neighbor +search on input matrix. Algorithm based on the N2 implementation of an approximate +nearest neighbor search using hierarchical @acronym{NSW, Navigable Small World} +graphs.") + (license license:asl2.0))) + (define-public r-network (package (name "r-network") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:18 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:18 +0000 Received: from localhost ([127.0.0.1]:46112 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakv-0001Ri-Jr for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:18 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:54725) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakp-0001QN-IV for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:12 -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=1677493745; x=1679308146; bh=HkiwVsjsYJi9RZ/5sV78x3i3hBSGXsMoSuJO96A3bsg=; b=g00Zmrlqz/J4 5JEYnQsOfbslLaKtSyQZcDy3GEZbHhqy4z4OGPO+VxKRcmubvl8+jZ+24qEodHdg Ywd3vaiFaZlnK3vQBSIbqy/7V0aI8qeDrJ2f3P/8t/2PSfT+URzdZ8i/xid8NBeI zibWMYf9+L5R1MaaWBX0iMnLxGn60UM= 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 7A812160157 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:05 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 05/13] gnu: Add r-leidenalg. Date: Mon, 27 Feb 2023 11:28:42 +0100 Message-ID: <20230227102850.18782-5-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10-2.199100-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeNTZ+DFCYZ6L6Pn cFCKybazRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRn8PhVj1fZ+6Ovj cPt7lSgOPyewSzonlQ/r8ztE1BNUXFA/vEqOUr49H4a2iJdV4MeOSS2dsOh9pU72YOAMDJjieAi CmPx4NwGmRqNBHmBvepuP9zg477pEqtq5d3cxkNRqXnrxrKCOXXz2rWAd+ccbEJzAmiQN5hGKAF gT6tgFAGm4GiR+m3eBPTK8cTqF7d61BZ2PJTcHYI6/uOY+4KjWR9NIHayOz1H/zrJEIGPrWDUEk BTZ8vOLxlyTCXQR4xioA5PA4dQuxuYpJR2kheXd+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.199100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 931BE625091C4C97D9E6CB0572611C733234BE8BB5FA8D77A49DEC5326BBFBF82002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-leidenalg): New variable. --- gnu/packages/cran.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index da2b2521a7..3784faa752 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23308,6 +23308,41 @@ (define-public r-leiden guaranteeing well-connected communities.\" .") (license license:gpl3))) +(define-public r-leidenalg + (package + (name "r-leidenalg") + (version "1.0.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "leidenAlg" version)) + (sha256 + (base32 "1z96zrsms93gspylmficaggb0xj94kq9rg3p2svdbb451jbga9an")))) + (properties `((upstream-name . "leidenAlg"))) + (build-system r-build-system) + (inputs + (list glpk + libxml2)) + (propagated-inputs + (list gmp + r-igraph + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-sccore)) + (native-inputs (list gfortran)) + (home-page "https://github.com/kharchenkolab/leidenAlg") + (synopsis "Leiden algorithm via an R interface") + (description + "This package implements an R interface to the Leiden algorithm, an iterative +community detection algorithm on networks. The algorithm is designed to converge +to a partition in which all subsets of all communities are locally optimally assigned, +yielding communities guaranteed to be connected. The implementation proves to be +fast, scales well, and can be run on graphs of millions of nodes (as long as they can +fit in memory).") + (license license:gpl3))) + (define-public r-patchwork (package (name "r-patchwork") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:18 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:18 +0000 Received: from localhost ([127.0.0.1]:46114 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakw-0001Rv-9L for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:18 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:41683) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakq-0001QP-B0 for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:12 -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=1677493746; x=1679308147; bh=6pGR/H6d2vzekEq4EpkW+oxEe6fEG7U5NexBPk8Jf08=; b=Z2pWS3cCouH9 OCl5XeFcMe8+kN+A11vcxA3TXvM1hDSIM9m6Cehq8mZlpGc5YvMMMnZWTtEpSvGy LtWihWdbtCqWB9uYwQ5mzFXWUk+6OmBlCaiZGOgWDql/7Vss8BGHPckVgvE2aFwk yhSSTwqPxzM5rMDfYMoDfpxJrITJcIU= 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 3634B16015F for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:06 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 06/13] gnu: Add r-drat. Date: Mon, 27 Feb 2023 11:28:43 +0100 Message-ID: <20230227102850.18782-6-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--5.602400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6sZaZ5UBQsocXjfR3d0weRkh03B1j/kTwNFz ikxQUUcu6Hd/enhcPQMiCi6ZMaQXn+fCnS6ApknzdCok3ibXlQeuLFZZYlisfHxPMjOKY7A+u65 UDD0aDgsRB0bsfrpPIXzYxeQR1Dvu9nWD8SGkvaKaLCZem3oyDi+vywNj0tSXicDICAIwbIX6iU TvELiFl X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.602400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 8210F13E2FD6B64018C5ECB64C2183A7576215B04A2E8344D827820B3FF2C4192002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-drat): 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 3784faa752..dbf98cdd81 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -6380,6 +6380,29 @@ (define-public r-lava variable models.") (license license:gpl3))) +(define-public r-drat + (package + (name "r-drat") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "drat" version)) + (sha256 + (base32 "191yxlj9jccakmz27g7n9izfcy19kj3fgnw4w6zl9iq66787qpm6")))) + (properties `((upstream-name . "drat"))) + (build-system r-build-system) + (native-inputs (list r-simplermarkdown)) + (home-page "https://github.com/eddelbuettel/drat") + (synopsis "'Drat' R archive template") + (description + "This package helps you with creation and use of R repositories via helper +functions to insert packages into a repository, and to add repository information +to the current R session. Two primary types of repositories are support: gh-pages +at GitHub, as well as local repositories on either the same machine or a local +network. Drat is a recursive acronym: Drat R Archive Template.") + (license license:gpl2+))) + (define-public r-drr (package (name "r-drr") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:31 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:31 +0000 Received: from localhost ([127.0.0.1]:46120 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWal8-0001Sd-LW for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:30 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:40091) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakt-0001Qa-Ux for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:16 -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=1677493747; x=1679308148; bh=W4koQ6UEihFXKLKU4e9J0pXtX0KdshlVwlbxP6xFdHA=; b=AVX7e+5evmQy pIQ9IH+K7g0JlvqCm6xNYqV+ZKY2Ake8hAwtBZhkORRQMiyFxvZx/s5ZowFpX7Lj P0ZZlcH53pBrziT30GTza0+ZfRu9e2YE6yRLEPM+ZLbu/98E3xe9aeOJoklqD0tu ZgXVar1IOJXAoYK/LXrXYZlss/X5Ri0= 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 F20F8160165 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:06 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 07/13] gnu: Add r-dendsort. Date: Mon, 27 Feb 2023 11:28:44 +0100 Message-ID: <20230227102850.18782-7-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10-1.070100-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEGQb gS2jMHPfRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v++F//Mn3a2w6Y5ZGw7wyeHU31 U0YBeWoJur4VwB2QBhOvctueKsC+N0N7DjAdxZNTi8zVgXoAltsIJ+4gwXrEtwrbXMGDYqV/x/F 0UMEoTu9i7bQL49QLr+z8Q0x0M9pjFRlvGDcpJCYH11Z98YXnRTjNq8sKSpTl2U9sb+6+uyLp+C x+pweKl5uhEUSIq0GLWyEfHH6RoHShCDgyssE8uo3yYJV8x0OrMUVc0s17dsX/q4TD2v7K1 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.070100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 24BBE92DD8A3A9FF8BD21CDFDCC9530C8C40EEF94ECD7325B5EF0613CB988BD52002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-dendsort): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index dbf98cdd81..d69d214d64 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5333,6 +5333,33 @@ (define-public r-dendextend ;; Any of these versions (license (list license:gpl2 license:gpl3)))) +(define-public r-dendsort + (package + (name "r-dendsort") + (version "0.3.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "dendsort" version)) + (sha256 + (base32 "0rs7y471wrhkgibxdmfh5xhp3pa004rrlm2w08b6qli5gq4im5d2")))) + (properties `((upstream-name . "dendsort"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/evanbiederstedt/dendsort") + (synopsis "Modular leaf ordering methods for dendrogram nodes") + (description + "The pacake represents an implementation of functions to optimize ordering +of nodes in a dendrogram, without affecting the meaning of the dendrogram. A +dendrogram can be sorted based on the average distance of subtrees, or based on +the smallest distance value. These sorting methods improve readability and +interpretability of tree structure, especially for tasks such as comparison of +different distance measures or linkage types and identification of tight clusters +and outliers. As a result, it also introduces more meaningful reordering for a +coupled heatmap visualization.") + ;; Any of these versions + (license (list license:gpl2 license:gpl3)))) + (define-public r-getoptlong (package (name "r-getoptlong") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:31 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:31 +0000 Received: from localhost ([127.0.0.1]:46122 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWal9-0001Sf-08 for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:31 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:45099) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakt-0001Qb-VK for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:16 -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=1677493747; x=1679308148; bh=TAr8bN4SBGRD6Z1o4oIBQknhryNnOw7burNXL93rkcQ=; b=S4arCkLFexxG lBqVcqo6foLziq6QEny8oYr9V88O0jDj/5BiwDoqmI3/EUUcFOrh0rzaTMUyYcTB iGs3DQ5hetKXUJqCcAhsub6+wWExC6mk02u2oCBaWUNwq7VwIiNd0V8LeXYFZRmp lFhxuUg/uTZoW5rMW0x6P7ubT2PTMYE= 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 DD477160167 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:07 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 08/13] gnu: Add r-pagoda2. Date: Mon, 27 Feb 2023 11:28:45 +0100 Message-ID: <20230227102850.18782-8-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10-0.515800-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIjG wx10ej9iRRa406V/YwyBUGewL2YXt3xSs/yDFAAwwLYk+NSxc5r4qCLIu0mtIKY5ZGw7wyeHyce sW0mt376cCvEBGezxXEtybYtfaziKvCGUW+fAEvCXVXMu1aPavF13okaUN2CbU72YOAMDJjieAi CmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP1xgyx3DOmb+S8+xOp7iNiN5JPLLt3Yh8nt1+GomUGE6 6fTYkRrQ6974UpoabFnisIEebihY9EVQskI952B2fE/EX8N0SZHM+4hpa/QfdxSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.515800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 71A0F95E5BFB674366D44CDEB83863A5A4F1ABF4CCC04F4FCF9DE6451751AACF2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-pagoda2): New variable. --- gnu/packages/cran.scm | 52 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index d69d214d64..e810924766 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2031,6 +2031,58 @@ (define-public r-pacman functions which can speed up workflow.") (license license:gpl2))) +(define-public r-pagoda2 + (package + (name "r-pagoda2") + (version "1.0.10") + (source + (origin + (method url-fetch) + (uri (cran-uri "pagoda2" version)) + (sha256 + (base32 "18ip8j5l5c3hqw1xsf5wnyas55i2mhk09phy68kjkjdgcymmpg7c")))) + (properties `((upstream-name . "pagoda2"))) + (build-system r-build-system) + (propagated-inputs + (list r-dendsort + r-drat + r-fastcluster + r-igraph + r-irlba + r-magrittr + r-mass + r-matrix + r-mgcv + r-n2r + r-plyr + r-r-utils + r-r6 + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress + r-rjson + r-rlang + r-rmtstat + r-rook + r-rtsne + r-sccore + r-urltools)) + (home-page "https://github.com/kharchenkolab/pagoda2") + (synopsis "Single cell analysis and differential expression") + (description + "The package offers functions for analyzing and interactively exploring large-scale +single-cell RNA-seq datasets. Pagoda2 primarily performs normalization and differential +gene expression analysis, with an interactive application for exploring single-cell +RNA-seq datasets. It performs basic tasks such as cell size normalization, gene +variance normalization, and can be used to identify subpopulations and run differential +expression within individual samples. pagoda2 was written to rapidly process modern +large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application +allows users to explore which gene expression patterns form the different subpopulations +within your data. The package also serves as the primary method for preprocessing +data for conos.") + (license license:gpl3))) + (define-public r-pals (package (name "r-pals") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:31 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:31 +0000 Received: from localhost ([127.0.0.1]:46124 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWal9-0001Sn-BQ for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:31 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:45845) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWaku-0001Qi-9X for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:17 -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=1677493748; x=1679308149; bh=vhvry3Oug6+QcJTtDU8K80p1dVPnS5xx1fe4zLPstvA=; b=beV6cjnm6tep cC//1yYps5ywA4Rtv06jStr7TSWrkCLPeKsPighz5NSSxnpacsA00Ly+eH9GWfIQ 7vrCtoo9m2mjWi9RB5Z4WfuR5okClYcyqITKAPLABJIsVVtgaTC2pUmV2NAEY5TK KS4gqPoEcv7RGGwS5DeMwFUKooEiq2c= 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 B9885160171 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:08 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:02 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 09/13] gnu: Add r-conos. Date: Mon, 27 Feb 2023 11:28:46 +0100 Message-ID: <20230227102850.18782-9-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--2.734900-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEN+a z/Eyz14URRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8ejl8XURi8fKY5ZGw7wyeHUug dhXQEiwM71P4XZynZYlc18FUgH1cwxzdZUAxpvx1H4a2iJdV4MRDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYXJ5h5eSCMT+A9xmMnWtx9B1i+4D/HQrfhDI4QrStZfrhtvx S77C2D1qtsBANBlnkTAxACcf30+b+HoWhTvAMM56mS2OwSL+jzHpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.734900-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 6616DCCC2E4E410CAA615E86CA5E663E57F9479CCEF5B7AC12F4E8CB98D768922002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/bioconductor.scm (r-conos): 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 bc3bd8c930..333df756c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5581,6 +5581,56 @@ (define-public r-complexheatmap self-defined annotation graphics.") (license license:gpl2+))) +;;This package depends on r-complexheatmap +(define-public r-conos + (package + (name "r-conos") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "conos" version)) + (sha256 + (base32 "1wdhb3jxh4id6xaghawzip8s264g9jxp4i5xy7jfhi67yfxszx6w")))) + (properties `((upstream-name . "conos"))) + (build-system r-build-system) + (propagated-inputs + (list r-abind + r-complexheatmap + r-cowplot + r-dendextend + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-igraph + r-irlba + r-leidenalg + r-magrittr + r-matrix + r-n2r + r-r6 + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress + r-reshape2 + r-rlang + r-rtsne + r-sccore +)) + (home-page "https://github.com/kharchenkolab/conos") + (synopsis "Clustering on network of samples") + (description + "This package wires together large collections of single-cell RNA-seq datasets, +which allows for both the identification of recurrent cell clusters and the propagation +of information between datasets in multi-sample or atlas-scale collections. Conos +focuses on the uniform mapping of homologous cell types across heterogeneous sample +collections. For instance, users could investigate a collection of dozens of +peripheral blood samples from cancer patients combined with dozens of controls, +which perhaps includes samples of a related tissue such as lymph nodes.") + (license license:gpl3))) + (define-public r-copywriter (package (name "r-copywriter") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:32 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:32 +0000 Received: from localhost ([127.0.0.1]:46126 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWal9-0001Su-Mi for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:32 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34303) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakv-0001Qw-Eb for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:17 -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=1677493750; x=1679308151; bh=KGr12m3TDH6tJkS6CuTNiyjs2puWExaHVZOHkYY2jeU=; b=XxRIJ8PhS+Uj udutHASxT5EZg6jqIhOyuQny7BatyoTeVHNfSREFxppT+dAbZAQ/u8eeml9cpwa6 gsw/TAouVDbGXmpfP1n1FHsqmKCEYaandbVheOGJ7CdkBUCsIdm7rF2ZREDsSTaL fMgU7OB+tr4Vn4yxO2uQdms6AEq/VW0= 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 3687D160177 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:10 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:02 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 10/13] gnu: Add r-conospanel. Date: Mon, 27 Feb 2023 11:28:47 +0100 Message-ID: <20230227102850.18782-10-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--2.227400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkECQG h5qJzqDbXt3JNptef3p4Zvg4N7yewiq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIEJ1hMCC63pYfEz RZ8UqjkrF+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2KlffUeErNKFJifXll gPnrPEFUk+7eUYdAi4xSQgPBynPT4YwppSH36p/WB6EZq1e5bSnFHAMTiwqZmxLoAcNNTt9PdtO GZ647e3I8jLGKSl8/0oQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.227400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: A48CE3B6B98585BFB66EFB1920EA9EBE8F1F84F34C90E3CD6BD180029EF544592002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-conospanel): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e810924766..fdbaf6ef56 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -23591,6 +23591,28 @@ (define-public r-harmony function and interfaces to external frameworks.") (license license:gpl3))) +(define-public r-conospanel + (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9") + (revision "1")) + (package + (name "r-conospanel") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kharchenkolab/conosPanel") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1zf0aj5d4iaxc3ghvjnaja5qby1avlmljzh94bpyvxbd359z9snn")))) + (properties `((upstream-name . "conosPanel"))) + (build-system r-build-system) + (home-page "https://github.com/kharchenkolab/conosPanel") + (synopsis "Package for conos data") + (description "Data used by conos") + (license license:gpl3)))) + (define-public r-covr (package (name "r-covr") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:32 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:32 +0000 Received: from localhost ([127.0.0.1]:46128 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWalA-0001T1-2B for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:32 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:49713) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakw-0001R9-LV for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:18 -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=1677493752; x=1679308153; bh=kK7vHHrdr24/hACyZtYkZTslEM1LUabU0B2virYCrNY=; b=N2PEQ+jEZHLD mEv/gSwBS8jrOec5+yya+8EdpFTfiGUwRhD0zBf6j0TBm26TGa3aM//Fnivtexe8 gC0whoRdLEdyblXjPViZ6Q1x5kCnDImLLq/gHVKvYRWYJFw5mHfTi9QICZIOxcM9 Zbea4y46Euc0xh2yau71qfnqYoo3YGY= 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 1B7DA16011B for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:12 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 04/13] gnu: Add r-sccore. Date: Mon, 27 Feb 2023 11:28:41 +0100 Message-ID: <20230227102850.18782-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--0.400400-5.000000 X-TMASE-MatchedRID: toN6SH028bX/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCyAkbY6/7arYC99T+uJIleRin8 0GPYQvJ/F+KCpGE37CJsoi2XrUn/Jn6KdMrRsL14qtq5d3cxkNRqXnrxrKCOXFNZvrbgGmIH6/r RmH7yfnPGkPN0XUwXyL/3FQcdprE/XCgvxehdbjWYdoN8+OB8LVpbhfV+B4egf0yVBQcER00FUh i5/kgQuDUEkBTZ8vOLxlyTCXQR4xioA5PA4dQuxuYpJR2kheXd+3BndfXUhXQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.400400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: B6EAEB4C8329D6CE4538D685EA5378FC838E4F0985C53EEAB71715FA6AFFE85D2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-sccore): New variable. --- gnu/packages/cran.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 184cbd6d7f..da2b2521a7 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -22401,6 +22401,48 @@ (define-public r-lintr code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.") (license license:expat))) +(define-public r-sccore + (package + (name "r-sccore") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "sccore" version)) + (sha256 + (base32 "12gm7pb6xbvf9kdsgl7ldw1c54ga9fgk99ps2kx2cq91q9m0ld4r")))) + (properties `((upstream-name . "sccore"))) + (build-system r-build-system) + (propagated-inputs + (list r-dplyr + r-ggplot2 + r-ggrepel + r-igraph + r-irlba + r-magrittr + r-matrix + r-pbmcapply + r-proc + r-rcpp + r-rcpparmadillo + r-rcppeigen + r-rcppprogress + r-rlang + r-scales + r-tibble + r-uwot + r-withr)) + (home-page "https://github.com/kharchenkolab/sccore") + (synopsis "Core utilities for single-cell RNA-Seq") + (description + "This package implements core utilities for single-cell RNA-seq data analysis. +Contained within are utility functions for working with @acronym{DE, differential +expression} matrices and count matrices, a collection of functions for manipulating +and plotting data via ggplot2, and functions to work with cell graphs and cell +embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP, +collapsing vertices of each cluster in the graph, and propagating graph labels.") + (license license:gpl3))) + (define-public r-scs (package (name "r-scs") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:32 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:32 +0000 Received: from localhost ([127.0.0.1]:46130 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWalA-0001T9-DP for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:32 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:44911) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakx-0001RA-C7 for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:19 -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=1677493753; x=1679308154; bh=8xXM0jUAaVqq6y3XpvZ7pKlHH0mxqnO8l4gEdWlTZN8=; b=hb+ozO2Q8itN LqUkkb4eXQ5E3yKzFcZH7WWV40M7gZ0BsCAi1G9kD5c822geBGlB2nPYiE29QXNL s+b07x8mZn9Md6RXYYq2LzZu7pP+0a7Tf/ypxxlAp274sexQkuOWMBw1urA5stLS 2PcTinvWdKmdzTDjtHnb6XFP3fQqaZI= 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 51D8E160123 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:13 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:02 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 11/13] gnu: Add r-p2data. Date: Mon, 27 Feb 2023 11:28:48 +0100 Message-ID: <20230227102850.18782-11-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--3.729400-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnf/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIyd mby1eQX7K1OIo1kOJjPuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/F0kjYVlocofPlAor2K6GjlIO VA+gJRdLF+KCpGE37CJsoi2XrUn/J8m+hzBStantdY+ZoWiLIm8K21zBg2KlffUeErNKFJidiuO 4jBx75o/85ynzNCesbUWZmgzdmw8akDJtSc96JVwUZaKn8M/RxvQfHU4RCdixmfaUBIyfnEXdeM nJY1YF6CO7twKbP8XkoQg4MrLBPLqN8mCVfMdDqzFFXNLNe3bF/6uEw9r+ytQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.729400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: AD51C5C13A7C3989D1FB59EAAD9DB0AE142674BEA3C857251EE3D05D76F80DC82002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-p2data): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fdbaf6ef56..517db893cd 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -33149,6 +33149,28 @@ (define-public r-seuratdata distributed as independent packages.") (license license:gpl3)))) +(define-public r-p2data + (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c") + (revision "1")) + (package + (name "r-p2data") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kharchenkolab/p2data") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hadrldldxvhqs43aqs3c88bqfgql3wcfkbll3jz7fh6z7p3x324")))) + (properties `((upstream-name . "p2data"))) + (build-system r-build-system) + (home-page "https://github.com/kharchenkolab/p2data") + (synopsis "Data for pagoda2") + (description "This package contains data used by pagoda2.") + (license license:gpl3)))) + (define-public r-phangorn (package (name "r-phangorn") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:33 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:33 +0000 Received: from localhost ([127.0.0.1]:46132 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWalA-0001TG-Ot for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:33 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:40135) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWaky-0001RD-3o for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:20 -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=1677493754; x=1679308155; bh=K1yLYEl8ka9VMlnn37CBL+9lR9WVVIDSZNZdpZEyGJo=; b=GiYky8YE9sXs iiy6ox8E5UqWGLgsBvskIOpT4uDaCK0k43tBLnq0En1Q42T+EcPGRw/lP4pLyLIL 4bV4uyeGn8JfBmisLmUQNeRfedowyeLeyyUKBit7HAIUDnpNEvfk7AYAetkTJ3bC T8f7A1T0smmsfO/J9OAOzX8kJx1XQ00= 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 0AD3516014E for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:14 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:02 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 12/13] gnu: Add r-pma. Date: Mon, 27 Feb 2023 11:28:49 +0100 Message-ID: <20230227102850.18782-12-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10--4.686400-5.000000 X-TMASE-MatchedRID: 54gb2yeIOXT/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEBKT GNKPwaynM9YQpZ+69TnoE3TAn9uEtiq+GZ9ZHxIhuW77/y896siFzNNPDc6umOCbuVI7hVbL1xv NmiS10Z7CHNu/5KBL8xJTjjs9yT6Yo8WMkQWv6iV3LAytsQR4e42j49Ftap9Eymsk/wUE4houm2 Z3hsbYctMPjmay26CM3DvnY7dvJgEEkqEwCdSIKN/+FIbaFInTTc0iNdCWjcbM6vsSREdDjLaNn W8IcGWlgnm7ZAxJyw+717qbAvfhL7TnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.686400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 781686D0980171CD748622235F8065E1C935D0C31068D1FFF5D191E775188B892002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-pma): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 517db893cd..61dcff7f12 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -905,6 +905,26 @@ (define-public r-googlesheets4 can read and write both the metadata and the cell data in a Sheet.") (license license:expat))) +(define-public r-pma + (package + (name "r-pma") + (version "1.2.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "PMA" version)) + (sha256 + (base32 "1rhiylm3jfarnqdkv7nwg536sgsa30ic80dk9byks9w0wf4mn59s")))) + (properties `((upstream-name . "PMA"))) + (build-system r-build-system) + (home-page "https://github.com/bnaras/PMA") + (synopsis "Penalized multivariate analysis") + (description + "This package performs penalized multivariate analysis: a penalized matrix +decomposition, sparse principal components analysis, and sparse canonical +correlation analysis.") + (license license:gpl2+))) + (define-public r-proj4 (package (name "r-proj4") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 05:29:33 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 10:29:33 +0000 Received: from localhost ([127.0.0.1]:46134 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWalB-0001TN-3I for submit@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:33 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34733) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWakz-0001RF-CN for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 05:29:21 -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=1677493754; x=1679308155; bh=5V6NHzRmL9zvIfc095tS8FQm9EGZPQEmzXf59/Cs9II=; b=UiR3AquHDDIC TdM6hnmZdnYVG4JfSqAvBsL0Y5EQrNXY8Y8M5EIwyRyCoyc/BUvt5I7j2ws/cLah 8VTTs9IDtaIGdGJsBm8sVZgs2MMpl28wKLJhG6mwz46tdHicXRACwZl05KUQUin6 0nzgRNiansf/a3i7LAsuFt4yr+pTrBs= 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 BB5A8160157 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 11:29:14 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 11:29:02 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH 13/13] gnu: Add r-rmumps. Date: Mon, 27 Feb 2023 11:28:50 +0100 Message-ID: <20230227102850.18782-13-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 In-Reply-To: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-AS-Result: No-10-0.392800-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEIsD mFQEq0bLRRa406V/YwyBUGewL2YXt8Z8zsjIitoJ71Wx2uUbPLfExmr5hqNL1jhndY84+Wc88Ez rj89e7mv25soaHGUfxlhuYD6rxoXGdYlaOEy4HBwvWfLf9uv1HJnaxzJFBx6vLX3qyf3ewG/KSK DFk38hb8X4oKkYTfsImyiLZetSf8lBgw5G4NYCZN9pjzubZ2rHwrbXMGDYqV+eVW/ZdL52jxA+/ 9WAFpucmjGLhEDft4vdntt0YoLWLlzFjF9gvVDxLk9sHY7/y22fohQiiN3/YQXQlX1+WHD3tq15 yEbuUuK3BTY3y8sepShCDgyssE8uo3yYJV8x0OrMUVc0s17dsX/q4TD2v7K1 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.392800-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27472.006 X-TM-SNTS-SMTP: 28E3F89FB84C2836A6FB7BE66828F6CB16806976B86D3FA0ECB4FB72B683C10D2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-rmumps): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 61dcff7f12..11939ee20f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -5866,6 +5866,32 @@ (define-public r-rmpi provides an interactive R manager and worker environment.") (license license:gpl2+))) +(define-public r-rmumps + (package + (name "r-rmumps") + (version "5.2.1-22") + (source + (origin + (method url-fetch) + (uri (cran-uri "rmumps" version)) + (sha256 + (base32 "18wqy82hwnbiwqcyldg8ci0jmxfiaj65ila0fjzzv40d3kl8hx76")))) + (properties `((upstream-name . "rmumps"))) + (build-system r-build-system) + (inputs (list zlib)) + (propagated-inputs (list r-rcpp)) + (native-inputs (list gfortran)) + (home-page "http://www.mumps-solver.org/") + (synopsis "Wrapper for MUMPS library") + (description + "Some basic features of @acronym{MUMPS, Multifrontal Massively Parallel sparse +direct Solver} are wrapped in a class whose methods can be used for sequentially +solving a sparse linear system (symmetric or not) with one or many right hand +sides (dense or sparse). There is a possibility to do separately symbolic +analysis, LU (or LDL^t) factorization and system solving. Third part ordering +libraries are included and can be used: PORD', METIS', SCOTCH'.") + (license license:gpl2+))) + (define-public r-lmoments (package (name "r-lmoments") -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 14:11:34 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 19:11:34 +0000 Received: from localhost ([127.0.0.1]:48831 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWiuL-00067d-LP for submit@debbugs.gnu.org; Mon, 27 Feb 2023 14:11:33 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21075) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWiuI-00067U-Tk for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 14:11:32 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677525087; cv=none; d=zohomail.com; s=zohoarc; b=EnfnpiF5NFChDZQ9WvF0eqt0dzprtHOLcw4WmxTdH8crnvNoEnB5NU7HjA1J9RDhp7ChfZv3QgXamvWBJ0ERa2VWM3ABgbr2/pMfkHDRaeg9Ptl+RxsqsdEAxs5j7jW1yGo/6zCvKYTGVC7OfE+xGae8sxXKtmd4LBASxGUIfH8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677525087; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=7gB26jxZBel4s/Nif0q/CZnAy1iV/U2S3VwzGSjcThM=; b=Z9lbE/ExBfkBYcpEIBowpSOOrwykpat9eLsTexgGd9JnV8A6l9BevrCic1yKJE6aK67hoIM2dP4WkEFILr6XUiOlQUqXLJBq8YCDJ08wQHH4t38AW9NLWqIIGoDj4ehISZ0/rnoMPJ3DSgZCRquZSzqWb7ekvjuOKAI5DOAhRR0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1677525087; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=7gB26jxZBel4s/Nif0q/CZnAy1iV/U2S3VwzGSjcThM=; b=gbtCyYTSzxOP4JCYXPKabT0Y3mHX0yQ6AACH0PICbQ3yhDLM79MSD/9wATDoWAm6 ho8QSnnIMIMl1PTpqe4AhxexGjsIAfxk94znw0DiwO8Ca0CV8Xc6+7wiFwwyTslyEOK vIkh+bbMLmAgckKFXNHFDuDsppgMCpcBlprTTjjQ= Received: from localhost (229-108-142-46.pool.kielnet.net [46.142.108.229]) by mx.zohomail.com with SMTPS id 1677525085226908.663462724414; Mon, 27 Feb 2023 11:11:25 -0800 (PST) References: <669c9a4b05f74824b87f3bb57fd23c98@mdc-berlin.de> <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61838] [PATCH 01/13] gnu: Add r-simplermarkdown. Date: Mon, 27 Feb 2023 20:10:17 +0100 In-reply-to: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87zg8yhqjp.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: 61838 Cc: 61838@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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/cran.scm (r-simplermarkdown): New variable. Thanks for the patch. This package=E2=80=99s DESCRIPTION file says that Pa= ndoc must be installed and available in the search path, yet this package does not have pandoc as an input. Would it be possible to patch the reference to the pandoc executable? --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 14:13:25 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 19:13:25 +0000 Received: from localhost ([127.0.0.1]:48835 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWiw9-0006Ax-4U for submit@debbugs.gnu.org; Mon, 27 Feb 2023 14:13:25 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21040) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWiw6-0006Ao-Qe for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 14:13:23 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677525200; cv=none; d=zohomail.com; s=zohoarc; b=CViOt+FFd116a9xQCZvrY6FAEyerEZ2C7IRKvWfOKjI8XMctu5tlPCs5mScAYUqRzEKexjrh2iRMpmZlkQehr6hpTA6clBDgOCCBkkQ0gTXomo+7i+LmnsH+6MMYY9qOFH2wwa6eX5uL0zKW+Cobgy76rxZrZ3kDMrQJ/Sw1WkQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677525200; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=oReBSFv29/oA5JDUZvTEmIVhKVi67dzdiskgMepmfR4=; b=Zhp/fgFnKnYAYiCyydB7nHQWi7ZJO40KE+NnXyisbw7E1bSv/pBguQENNiACYtQ32QYbuCZMqJx3zx34m6gDeRde2uMGN2lF/hWN4vCssI5ldeDfa8FH+X1jpQSXeNtMBbYkiJ1fVfhCOULXs7t2CSb3UeMcesg1SyEhk4S13Ko= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1677525200; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=oReBSFv29/oA5JDUZvTEmIVhKVi67dzdiskgMepmfR4=; b=OXW7Eu6IgBePl78yIih+0kpWym2sMtkh7VQ4BZ1KWCbdm2l4n5YJguWVSAcjhGCw HAl4wfXpVemlWlg1rRoOa+584yMWQP24DZVu4b2xJzSr9cuLlkENDUrO90SFZAiDBQn BZHsCu/ZMT6We496ZZhO1jP2OxQUNbdT+XjE4D+w= Received: from localhost (229-108-142-46.pool.kielnet.net [46.142.108.229]) by mx.zohomail.com with SMTPS id 1677525196856308.7763333412945; Mon, 27 Feb 2023 11:13:16 -0800 (PST) References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> <20230227102850.18782-2-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61838] [PATCH 02/13] gnu: Add r-rcppspdlog. Date: Mon, 27 Feb 2023 20:12:13 +0100 In-reply-to: <20230227102850.18782-2-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87v8jmhqgl.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: 61838 Cc: 61838@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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/cran.scm (r-rcppspdlog): New variable. [=E2=80=A6] > + (synopsis "R and C++ interfaces to 'spdlog' C++ header library for l= ogging") Please remove the single quotes. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 14:14:18 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 19:14:19 +0000 Received: from localhost ([127.0.0.1]:48839 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWix0-0006Cl-Hm for submit@debbugs.gnu.org; Mon, 27 Feb 2023 14:14:18 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21081) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWiwy-0006Cc-Nb for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 14:14:17 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677525254; cv=none; d=zohomail.com; s=zohoarc; b=N1Gf8rribmpNCgoc0Mcl+e05gT4Ozbshi7qWo1RXCPpC+SXnk+AGaA8KEg5NGy42sfrU2oPH77F6/MlzwOBkqtcev/iCnUmZ6aOM+viyvguCPNrv+S2tdzwNI6/dBq3NdtsN3luFC3aeqsSp37KrdRNnA1JJis+9gUYF38QRw1o= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677525254; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=1pmUIpiMgF1K/WNki7INAchsfQFxlAJU8r4HE1Ms48Y=; b=U9BbwlEgjrzymIqctazaimFo7YI+jowdgqNbzkeWybiRaUPR60M91mbfpWauomI2RjDU4KBDGsthlfTE8OVfdAeRy67zaAb24F9uz2MFz6X4mGfPhyshxyMUi/KGZ5RV/Q8JHhD0CTInCWEfhYUR/SMEQgr9b1llQkEFO80E8O0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1677525254; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=1pmUIpiMgF1K/WNki7INAchsfQFxlAJU8r4HE1Ms48Y=; b=XdkhRK62sy2nfM/wqsAaM9bukQGsEEbKd/Uw+FdU6LebDhQtWtvunN4NASv+1ycv LsThlPqdm8Qk/bk8J0O6T9Yb43gd5Z0qiKO0CvKFXE4srG9MPsFH/ahA3KVCi0SxNdh jNRAqCJNHkXjy9bWsY5mL34HP18L6eBCX9k6VOEM= Received: from localhost (229-108-142-46.pool.kielnet.net [46.142.108.229]) by mx.zohomail.com with SMTPS id 1677525253388706.5912645323494; Mon, 27 Feb 2023 11:14:13 -0800 (PST) References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> <20230227102850.18782-3-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61838] [PATCH 03/13] gnu: Add r-n2r. Date: Mon, 27 Feb 2023 20:13:41 +0100 In-reply-to: <20230227102850.18782-3-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87r0uahqf1.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: 61838 Cc: 61838@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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/cran.scm (r-n2r): New variable. [=E2=80=A6] > + (description > + "This package implements methods to perform fast approximate K-near= est neighbor > +search on input matrix. Algorithm based on the N2 implementation of an = approximate > +nearest neighbor search using hierarchical @acronym{NSW, Navigable Small= World} > +graphs.") Please use complete sentences. The second sentence is a fragment. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 14:15:24 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 19:15:24 +0000 Received: from localhost ([127.0.0.1]:48843 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWiy4-0006FB-28 for submit@debbugs.gnu.org; Mon, 27 Feb 2023 14:15:24 -0500 Received: from sender3-of-o59.zoho.com ([136.143.184.59]:21922) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWiy1-0006F2-Ni for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 14:15:22 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677525315; cv=none; d=zohomail.com; s=zohoarc; b=CAsBYRaKES2yhebtTTxtnsvY/wDBhJNfB3KbhikwY39iX3L147M6Et0URAY1LuyET9CmLB6CU4qPaeSorAjS1yRJfdsuCFjX34MHp7iAb4k0th3y7gLBEmx4/wU898opmooUQ0MfZKOO+6rXSjWB+Q9KAMxxqZVD8AXud1wYZCg= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677525315; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=RZuh2550dq7ZLhZmZzKQvb6H3lznNVGhUN7RD+OSsQg=; b=RZy12Ax0J2ugES+GaJp2rOpM9OM+EkKrtazoF/ou07AERM/shDoaoQUTh0hVEdZHsa6Q8oEtblcH5JEbbbUckOSOuQ3ZZaww1Oxn+GHS181qmEwWxCuMSKRXL8oHuCxHs1qFTrsLoLuaODs9OYlQbNUoyIKgU3y1jatHw1i4LcU= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1677525315; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=RZuh2550dq7ZLhZmZzKQvb6H3lznNVGhUN7RD+OSsQg=; b=V7NzHnIVIfMPcEhPf6vpgWDgBnb2F4WNON9LrXOZU1LI2DeK2HbaA/64ITnxTVKT IiQnZ4RFD+ZBTlM0meDgNoAgzKMOu4OyUvqtgr1ae5WFaluJxJDbN9OXJ6LIYJAprPb bfj8yv8HVD7Iu+XhJS3+jJdv91LsWkykQOgRCFaQ= Received: from localhost (229-108-142-46.pool.kielnet.net [46.142.108.229]) by mx.zohomail.com with SMTPS id 167752531195960.79268174621268; Mon, 27 Feb 2023 11:15:11 -0800 (PST) References: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> <20230227102850.18782-4-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61838] [PATCH 04/13] gnu: Add r-sccore. Date: Mon, 27 Feb 2023 20:14:57 +0100 In-reply-to: <20230227102850.18782-4-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87mt4yhqdf.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: 61838 Cc: 61838@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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/cran.scm (r-sccore): New variable. LGTM --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 15:43:11 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 20:43:11 +0000 Received: from localhost ([127.0.0.1]:48934 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWkL0-0002dd-TG for submit@debbugs.gnu.org; Mon, 27 Feb 2023 15:43:11 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:52533) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWkKx-0002d7-I4 for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 15:43:09 -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=1677530580; x=1679344981; bh=suFI9wRzNczR93r QrR5U7+P7LzFvwqwPgnmjOvQHEOE=; b=P9fzB1IZ4WnCWuDx593LxrOYZzSZQiS RLUblcfP74ALtoSQX4BLpFpiNrdEQXmOpuc90V0tmXVTkr29TQRWCV2JewmOczZY DeCg+MerqUr3SbrP9/9iEImvAcOIBfpU1mCSYA+Q5rcy9Ch3bz2p0odXrwSb5Ton hWNrX2hW71BQ= 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 F04A6160167 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 21:42:59 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 21:42:59 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH v2 01/13] gnu: Add r-simplermarkdown. Date: Mon, 27 Feb 2023 21:42:49 +0100 Message-ID: <20230227204249.1906-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27474.002 X-TM-AS-Result: No-10--7.317600-5.000000 X-TMASE-MatchedRID: I6rpFm0lrcP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6GFMYlDUzwr0XjfR3d0weRh7W0X9FnZcMeA9 iB1Lee2SGsZX0q3FpiOhAZQXEXXZuqOJ+h+s5fKarm7DrUlmNkIAy6p60ZV62yA7duzCw6dLdB/ CxWTRRu92KvEVWmYr1lbg6sACdqpJcs03tjyrcUwhPf3w0HmcEKTRwsAnBGrKRSJzNOd/VMA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.317600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27474.002 X-TM-SNTS-SMTP: 2E325AF5032A1E2D3C3C7727BEB1CAAB1E5E3DA00037562B05A06DCFBB8376B02002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-simplermarkdown): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c80e98134a..965b10c3a5 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -9652,6 +9652,30 @@ (define-public r-signal It also includes interpolation functions.") (license license:gpl2))) +(define-public r-simplermarkdown + (package + (name "r-simplermarkdown") + (version "0.0.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "simplermarkdown" version)) + (sha256 + (base32 "069pgx5m22rdqa21lyn5zqm9ym3g7w6z1d2wjwms8b1f2cp6266g")))) + (properties `((upstream-name . "simplermarkdown"))) + (build-system r-build-system) + (propagated-inputs + (list pandoc + r-rjson)) + (home-page "https://github.com/djvanderlaan/simplermarkdown") + (synopsis "Simple engine for generating reports using R") + (description + "This package runs R-code present in a pandoc markdown file and includes the +resulting output in the resulting markdown file. This file can then be converted +into any of the output formats supported by pandoc. The package can also be used +as an engine for writing package vignettes.") + (license license:gpl3+))) + (define-public r-gsubfn (package (name "r-gsubfn") base-commit: 4db367f8ae4e704784ced52b552437ca00b94b89 -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 16:18:16 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 21:18:16 +0000 Received: from localhost ([127.0.0.1]:49007 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWksy-00067G-5P for submit@debbugs.gnu.org; Mon, 27 Feb 2023 16:18:16 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:42837) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWksu-00066x-3f for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 16:18:15 -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=1677532684; x=1679347085; bh=v5Anr0pK+/PIFXe BXrQcc+oZ8LBZd8UVDGZV7ZcUj+U=; b=TyrlNIoe3k7RY5d95RunY/Z7PWnhYLv 0fWCr2GPcYFHYzmB+ZnPduUs7CfnquI882BWS3u5SKw3DHN7M4RFQmofJJuLkXcs Jw7Qb2o6PWa9WrQ4bp3VQyY0MAoVMmNISreRrzz2E7VJj83SGNKQCYuFhsd7LwTx jcIg9TNxAvMk= 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 E1EA9160167 for <61838@debbugs.gnu.org>; Mon, 27 Feb 2023 22:18:02 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Mon, 27 Feb 2023 22:18:01 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH v2 02/13] gnu: Add r-rcppspdlog. Date: Mon, 27 Feb 2023 22:17:44 +0100 Message-ID: <20230227211744.1978-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27474.003 X-TM-AS-Result: No-10--7.783200-5.000000 X-TMASE-MatchedRID: GQw6Xh/XS6X/R1NSMc2qCRIRh9wkXSlFwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9+tO36GYDlsgKJcjtscVQF79F PP6Y5dX00pm3+L2DmzMJcQxieZN8ITyoytgYhFtdwKlYjOzXY1QK0ZgbTOeKU5lhx0mBJyPEqyb XRNOEMIhfSNx4Mm0chfpXHFYWCQdejxYyRBa/qJcFwgTvxipFa9xS3mVzWUuCgZHIBpyeFpmeXH uTUfSNcmItMly8fgKdVK5KFgfJJDS5X6SBIy3ubftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.783200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27474.003 X-TM-SNTS-SMTP: 6AABA8851665CA65F36A3256F29E91E3BACF75772EEBF1CA6814516E9FBE41712002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-rcppspdlog): New variable. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) Changes since v1: - [synopsis]: removed single quotes. diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 965b10c3a5..f5dc9c3980 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -4992,6 +4992,30 @@ (define-public r-rcppml factorization and divisive clustering for large sparse and dense matrices.") (license license:gpl2+))) +(define-public r-rcppspdlog + (package + (name "r-rcppspdlog") + (version "0.0.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "RcppSpdlog" version)) + (sha256 + (base32 "1nan0hm49xdl2l1lskm1jf01clfh7aw2v6h57j35qysvg8219fcx")))) + (properties `((upstream-name . "RcppSpdlog"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp)) + (native-inputs (list r-simplermarkdown)) + (home-page "https://github.com/eddelbuettel/rcppspdlog") + (synopsis "R and C++ interfaces to spdlog C++ header library for logging") + (description + "The spdlog library is a widely-used and very capable header-only C++ library +for logging. This package includes its headers as an R package to permit other R +packages to deploy it via a simple @code{LinkingTo: RcppSpdlog}. As of version +0.0.9, it also provides both simple R logging functions and compiled functions +callable by other packages.") + (license license:gpl2+))) + (define-public r-rcppthread (package (name "r-rcppthread") base-commit: 4db367f8ae4e704784ced52b552437ca00b94b89 prerequisite-patch-id: edae0018d5bb597484681580e87ff4e84d3e4f97 -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Feb 27 18:37:44 2023 Received: (at 61838) by debbugs.gnu.org; 27 Feb 2023 23:37:44 +0000 Received: from localhost ([127.0.0.1]:49208 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWn3v-0004Nl-Mo for submit@debbugs.gnu.org; Mon, 27 Feb 2023 18:37:43 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:35117) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pWn3r-0004NS-5M for 61838@debbugs.gnu.org; Mon, 27 Feb 2023 18:37:42 -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 :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1677541051; x=1679355452; bh=xpEmuGiR036TO6W lCMFwizZcEl4aIyzbjr7M7LUkqsU=; b=fcf1r31iCkuJBpmQSRoTl+N11FVupGN gWPTns6R5mwlCA9n8GG+NctVwHBCJOBR3BV2GL8Eggd6eXhxgJQXMITnpiHTPbEQ Fv7EZWq4vBhSzoKwvAx0BGnfYQuUkmIHxEPEHPXBg2Lq7MkI/UFxhnjMNiTBANna YgCSARCB+z34= 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 6C09D300195 for <61838@debbugs.gnu.org>; Tue, 28 Feb 2023 00:37:30 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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; Tue, 28 Feb 2023 00:37:29 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <61838@debbugs.gnu.org> Subject: [PATCH v2 03/13] gnu: Add r-n2r. Date: Tue, 28 Feb 2023 00:37:16 +0100 Message-ID: <20230227233716.2455-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 X-Debbugs-Cc: rekado@elephly.net Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27474.003 X-TM-AS-Result: No-10--2.184600-5.000000 X-TMASE-MatchedRID: a3KJLn6RIiL/R1NSMc2qCdfeP+V/VXwsdG11gm9qhi4li8Y5a0svL78F Hrw7frluf146W0iUu2vNs+hSjQLHECq+GZ9ZHxIhuW77/y896siFzNNPDc6umBHfiujuTbedCTE bKh6GrsEF2dkz2WOwqgKguJ8dND77+wOdDq3DYSHjpxdo/JwVm8oioCrSMgeK7rencS+jsJgjL8 WDWZGeoqEbr6VH4TuZmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5fB5Wk2oJGHXV6o5 oQSXoBCJH7HzNMBQY0ripNbToAUhAGWEAqI1/jKVZxxGQafovVFdJd49zQDPE+Q9lTIoWXygLtN +XVTSX0NQSQFNny84vGXJMJdBHjGKgDk8Dh1C7G5iklHaSF5d37cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.184600-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27474.003 X-TM-SNTS-SMTP: 392499B802896792CEEA747C4BDA9FBF29D100058A01BADAA160C1889429341B2002:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 61838 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: -3.3 (---) * gnu/packages/cran.scm (r-n2r): New variable. Changes from v1: - [description]: Changed the description after the Ricardo's observation. I hope that this is solve the issue. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f5dc9c3980..29f11bf3de 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8334,6 +8334,32 @@ (define-public r-tinytest ") (license license:gpl3))) +(define-public r-n2r + (package + (name "r-n2r") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "N2R" version)) + (sha256 + (base32 "12bv7xx6j6222qgpv6g61i68017fz0x6fjg9a9k5yhgw3zk05hpk")))) + (properties `((upstream-name . "N2R"))) + (build-system r-build-system) + (propagated-inputs + (list r-matrix + r-rcpp + r-rcppeigen + r-rcppspdlog)) + (home-page "https://github.com/kharchenkolab/N2R") + (synopsis "Fast and scalable approximate k-Nearest Neighbor search methods") + (description + "This package implements methods to perform fast approximate K-nearest neighbor +search on the input matrix. The algorithm is based on the N2 implementation of an +approximate nearest neighbor search using hierarchical @acronym{NSW, Navigable Small +World} graphs.") + (license license:asl2.0))) + (define-public r-network (package (name "r-network") base-commit: 4db367f8ae4e704784ced52b552437ca00b94b89 prerequisite-patch-id: edae0018d5bb597484681580e87ff4e84d3e4f97 prerequisite-patch-id: fe2fd38a8a277bb9352431960ff6322e66f56895 -- 2.39.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 06:13:26 2023 Received: (at 61838) by debbugs.gnu.org; 1 Mar 2023 11:13:27 +0000 Received: from localhost ([127.0.0.1]:52847 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXKOk-0003nV-Lo for submit@debbugs.gnu.org; Wed, 01 Mar 2023 06:13:26 -0500 Received: from sender3-of-o59.zoho.com ([136.143.184.59]:21955) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXKOi-0003nH-3A; Wed, 01 Mar 2023 06:13:24 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677669200; cv=none; d=zohomail.com; s=zohoarc; b=Qd8mYUMd+r7G1g70MAFSHRYxoTHVCkjAGnCqI6mvKQMEtp6ggqe5DR1UX29mnAl1Eljjz0TgZTTEma7FdkBBibNyRyb/dQRDYhdi9Exh2gZThiBV6I/AT+D/AVuR0+kkBnonOTD6WVdsOojGaqucZJXHRAQLi58l0S4WiFq4KkE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677669200; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=n4whVXy2Ca+eQ0mB4ythHKatw9ykSTCrS+4FEK6ZtoE=; b=kPx2xBLrWBE3qMorE4rvLYvar2ZEA5BnLMAlUZAw8AaBIhRJt7/njgVNpYzGCxg8OvEh6oSr+qaKD3NfV6pBLIBv+ySaQiC/2jK22Pz9xz5J/8dlq5udBV0a3CEdYcUwDjIHztDoBLQ1zwZm2BTqx50kQmQQSQFQT1swdGqCF64= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1677669200; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=n4whVXy2Ca+eQ0mB4ythHKatw9ykSTCrS+4FEK6ZtoE=; b=DuHZcuozQoRR4fGTy1SmyyW1SUgfva1FvZkE6Cukpd/fD089tGNTgVQ6mYgJtyJ/ CGKsgvBb0DACk41N5EtInX64YMFTMByXs8soph2xGXgZjgSpX10Q+LchkerJwBI+GI4 XyCw49XL0oT8MOxM4a9f17Uoi0yfNPeyDodnnMGA= Received: from localhost (i5E862DA7.versanet.de [94.134.45.167]) by mx.zohomail.com with SMTPS id 1677669196511271.7924708518607; Wed, 1 Mar 2023 03:13:16 -0800 (PST) References: <669c9a4b05f74824b87f3bb57fd23c98@mdc-berlin.de> <20230227204249.1906-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61838] [PATCH v2 01/13] gnu: Add r-simplermarkdown. Date: Wed, 01 Mar 2023 12:07:20 +0100 In-reply-to: <20230227204249.1906-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87sfeog1x2.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: 61838 Cc: debbugs-submit@debbugs.gnu.org, 61838@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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/cran.scm (r-simplermarkdown): New variable. Thanks for the update. Turns out we cannot easily patch references to the pandoc executable. I tried this: --8<---------------cut here---------------start------------->8--- (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'patch-pandoc-invocations (lambda* (#:key inputs #:allow-other-keys) (let ((pandoc (search-input-file inputs "/bin/pandoc"))) (substitute* '("R/mdtangle.R" "R/mdweave.R" "R/mdweave_to.R") (("'pandoc ") (string-append "'" pandoc " "))) (substitute* "R/has_pandoc.R" (("Sys.which\\(\"pandoc\"\\)") (string-append "\"" pandoc "\""))))))))) --8<---------------cut here---------------end--------------->8--- This works, but the resulting output no longer has any references to /gnu/store/=E2=80=A6-pandoc=E2=80=A6/bin/pandoc. That=E2=80=99s because no= ne of these files make it to the output. Instead they all seemingly get squished into a pair of simplermarkdown.rdx and .rdb files, which are compressed. So it is safer to propagate pandoc. This may point to a general problem with the r-build-system that we may need to investigate later. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 01 08:22:15 2023 Received: (at 61838-done) by debbugs.gnu.org; 1 Mar 2023 13:22:15 +0000 Received: from localhost ([127.0.0.1]:52979 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXMPP-0001RH-1w for submit@debbugs.gnu.org; Wed, 01 Mar 2023 08:22:15 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21071) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pXMPN-0001R8-Th for 61838-done@debbugs.gnu.org; Wed, 01 Mar 2023 08:22:14 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1677676930; cv=none; d=zohomail.com; s=zohoarc; b=giphkMu5tOrFO3GUG6eiUeOaN0rj/N1R18r4KoHHFCvhXfVLlj/nHFIUhHpt2CGXAcxgP1uARJJpo+4HKyNgIukV4wY4yGu/nexpLz2AZWTAnjaaZ7Eg0C9Lu0G38iwGEvwNBScdgubgSgIpssNVst96KzVTxRqHHuDXbAccACc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1677676930; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=BiJIj49ZHkh5mo98SjNIZrwe7JS3k5bIjfN2wqUOKUg=; b=GBgtLwceIxxYQPsPKYdRSEVj1FvuRFT1IhiVlUyyX4e2dWq8iPr7gqaJfNdfWbaXtBvt8RFyT5cQMSu1OG8OGosHuZmYC7x2czkTyvKHzYIHJmBfXvQ+74t1ULPoZw8DyHmQRyfp8IngCEMFwqr0jFV4KJGPAwLpKcRSLO3W0ug= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1677676930; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=BiJIj49ZHkh5mo98SjNIZrwe7JS3k5bIjfN2wqUOKUg=; b=hqmbgWTIqJCVOcNCIRup1Sv9OzO3ja19IMTHjjVaj027HzrzjxS9CD6CO9pcmsyp srN2Tvkg5REM9BibZk/6tSqQMi4i6rmbjiCRxsQl2moMdwzRA5aDE9b42B6TkJAVk1J Iixhl4ovsixRu+vB9IOVphsE306t24FsM1sNjwDM= Received: from localhost (i5E862DA7.versanet.de [94.134.45.167]) by mx.zohomail.com with SMTPS id 16776769289821005.9986953032486; Wed, 1 Mar 2023 05:22:08 -0800 (PST) References: <669c9a4b05f74824b87f3bb57fd23c98@mdc-berlin.de> <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#61838] [PATCH 01/13] gnu: Add r-simplermarkdown. Date: Wed, 01 Mar 2023 14:20:24 +0100 In-reply-to: <20230227102850.18782-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87o7pcfvya.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: 61838-done Cc: 61838-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) I=E2=80=99ve applied this series with a number of changes, not limited to t= he following: - moved non-CRAN packages to bioinformatics.scm (r-conospanel, r-p2data) - reformatted descriptions - fixed typos - corrected license of leidenalg - removed extraneous single quotes All pushed with the last commit f01b5299db6031174f05124b843c936388cd872a. Thanks! --=20 Ricardo From unknown Sun Jul 27 00:27:06 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Thu, 30 Mar 2023 11:24:08 +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