From debbugs-submit-bounces@debbugs.gnu.org Sat May 18 05:50:10 2024 Received: (at submit) by debbugs.gnu.org; 18 May 2024 09:50:10 +0000 Received: from localhost ([127.0.0.1]:60682 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s8Ghd-0000ew-Aa for submit@debbugs.gnu.org; Sat, 18 May 2024 05:50:10 -0400 Received: from lists.gnu.org ([209.51.188.17]:60052) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s8EqO-00076a-8u for submit@debbugs.gnu.org; Sat, 18 May 2024 03:51:05 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1s8EqJ-0002K7-RX for guix-patches@gnu.org; Sat, 18 May 2024 03:50:59 -0400 Received: from mail-200162.simplelogin.co ([176.119.200.162]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1s8EqF-000431-Cr for guix-patches@gnu.org; Sat, 18 May 2024 03:50:57 -0400 ARC-Seal: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1716018650; cv=none; b=Jpq5j6Rz+4weQeWMel3QIwUtrQOMx+0K3roktYIi5eVGvfzZJDxoeGsEdajfN6HbpVztIWB/10X9koHb+Q6fkT0j4IjY4NzL9xSsM7FIkF68xMkap3SaN/HeKxsjLI4B9GAYVBoaCrDqAnFrBBX/HohFeEOgYKtpVwM+w5QCOIOVBWkJa0Zm4qyH+IjlTQHUbqcGxp8TO//THjVsH5tQGR6LY3PTyk1Hx96l1ODlTx/CYFhvqxIV3rXMVohUn9ta9U/OgwqNhOsKYnYBN2FnmVBVPvFY7DMzdyP0cs8/rJJhvhVkDqlL5WfVQ+Rq+St9sPj1QvyKS8NmLBq2rc94pg== ARC-Message-Signature: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1716018650; c=relaxed/simple; bh=oTBWDJulpADsT4o21nCW3Ns4K5JLcehGUUx9QFkDnRw=; h=Date:Subject:From:To:Cc; b=tgxQwC9SRnbaecwBIU4cdPKgoYDtvO0nkINyIM0WlgaAn+Ws7zM++fPgvBGXO16T6n/m/AiKDQQ4lF5auLAtgBzsWcUVcP6Cnuc0lqZEeVpE4vIyLbONpenjmcRvkRgSHf5rcyWvbHDIcMzfxYIfGi1aimNa6Sp/oIV3WzuLAU+jDB0zGacLsY1Oa+UsuRCxnqZRfTW+f129l53RA4Ujb37exDbnjWhnn+FH48zZNc0kra5djvrGIC7kw1NvDGQBb6VwQVWI1rBpQ4MxUZ9uzjqZ1FdP1rujmUMXJL/IBxtrDKPLMKA4xmD89Ys+GArMEn20cBeGIPBxCu7lfIxo6A== ARC-Authentication-Results: i=1; mail.protonmail.ch DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mawumag.com; s=dkim; t=1716018650; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=l8Z0nJKsqnKJgKbcL3G8LldWO7XfmkL0TBlK4U1MG/s=; b=AU8E6G6nx3vhSbZnUQt0Gw68rGY209nRf2kehUle/Bu+POOg1BavVuuy7Vi3trn/eHpUOH bJoAJiFUS8WtLeXV/MiCtGrwuRlt7mJZYbi8EgBpUdMImeIboBzlu16BoK83UFdm2aN8LQ 0jeug3OyOKc3v8poLThOR618xmqmhPM= Date: Sat, 18 May 2024 07:50:46 +0000 Subject: [PATCH] Added r-mcview MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable From: guix@mawumag.com To: guix-patches@gnu.org Message-ID: <171601865003.8.3299177765362446936.333610631@mawumag.com> X-SimpleLogin-Type: Reply X-SimpleLogin-EmailLog-ID: 333610632 X-SimpleLogin-Want-Signing: yes Received-SPF: pass client-ip=176.119.200.162; envelope-from=sl.lmysyibtgmztmmjqgyztelbagezdkmbtheyf2.r23xvxhoioo6i@mawumag.com; helo=mail-200162.simplelogin.co X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.6 (/) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Sat, 18 May 2024 05:50:05 -0400 Cc: rekado@elephly.net 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: -1.6 (-) >From b6eec887067b4c4697fad3cae4f11fabc6330a86 Mon Sep 17 00:00:00 2001 From: Marco Baggio Date: Sat, 18 May 2024 09:23:07 +0200 Subject: [PATCH] Added r-mcview Change-Id: I377b7fd2256215ddcad73f4263bab251bd4319cd --- I added the package MCView, used to generate shiny apps for metacell models= , as well as dependencies not yet present in the official Guix repository. --- gnu/packages/bioinformatics.scm | 314 ++++++++++++++++++++++++++++++++ 1 file changed, 314 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 6aa35710e5..a696a5df29 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12228,6 +12228,320 @@ (define-public r-shinycell single-cell data.") (license license:gpl3)))) =20 +(define-public r-mcview + (let ((commit "85a61fe6efa241ac72f79fb965c3227538ead518") +=09(revision "1")) + (package + (name "r-mcview") + (version (git-version "0.2.28" revision commit)) + (source + (origin +=09 (method git-fetch) +=09 (uri (git-reference +=09 (url "https://github.com/tanaylab/MCView") +=09 (commit commit))) +=09 (file-name (git-file-name name version)) +=09 (sha256 +=09 (base32 "187q6qy8ss0g6h3c0ckw9ypq8615bk5yypfl5l4rq6dzaflm4iba")))) + (properties `((upstream-name . "MCView"))) + (build-system r-build-system) + (propagated-inputs (list r-anndata +=09=09=09 r-cachem +=09=09=09 r-chameleon +=09=09=09 r-circlize +=09=09=09 r-cli +=09=09=09 r-colourpicker +=09=09=09 r-cowplot +=09=09=09 r-dplyr +=09=09=09 r-dt +=09=09=09 r-fastcluster +=09=09=09 r-forcats +=09=09=09 r-fs +=09=09=09 r-furrr +=09=09=09 r-future +=09=09=09 r-gert +=09=09=09 r-ggplot2 +=09=09=09 r-ggtext +=09=09=09 r-glue +=09=09=09 r-golem +=09=09=09 r-htmltools +=09=09=09 r-markdown +=09=09=09 r-matrix +=09=09=09 r-matrixstats +=09=09=09 r-pkgload +=09=09=09 r-plotly +=09=09=09 r-promises +=09=09=09 r-purrr +=09=09=09 r-qs +=09=09=09 r-rintrojs +=09=09=09 r-rlang +=09=09=09 r-rmarkdown +=09=09=09 r-scales +=09=09=09 r-shiny +=09=09=09 r-shinybusy +=09=09=09 r-shinycssloaders +=09=09=09 r-shinydashboard +=09=09=09 r-shinydashboardplus +=09=09=09 r-shinyjqui +=09=09=09 r-shinyjs +=09=09=09 r-shinywidgets +=09=09=09 r-slanter +=09=09=09 r-tglkmeans +=09=09=09 r-tgstat +=09=09=09 r-tgutil +=09=09=09 r-tibble +=09=09=09 r-tidyr +=09=09=09 r-umap +=09=09=09 r-viridis +=09=09=09 r-waiter +=09=09=09 r-yaml +=09=09=09 r-zip)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tanaylab/MCView") + (synopsis "Shiny App for Metacell Analysis") + (description + "MCView creates a shiny-app facilitating interactive exploration an= d annotation +of metacell models. Metacell itself is described +[here](https://github.com/tanaylab/metacells/blob/master/vignettes/Metacel= ls_Vignette.ipynb). + You can also explore examples of MCV output for +[PBMC](https://tanaylab.weizmann.ac.il/MCV/PBMC) and [Mouse +organogenesis](https://tanaylab.weizmann.ac.il/MCV/MOCA) on the Tanay grou= p +server.") + (license license:expat)))) + +(define-public r-chameleon + (package + (name "r-chameleon") + (version "0.2-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "chameleon" version)) + (sha256 + (base32 "0a3azp0zaakpqqx0pp94hkj3vgb2apnf8gb5ga0as4i8lrn9dz8i")))) + (properties `((upstream-name . "chameleon"))) + (build-system r-build-system) + (propagated-inputs (list r-clue r-ggplot2 r-umap)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=3Dchameleon") + (synopsis "Automatic Colors for Multi-Dimensional Data") + (description + "Assign distinct colors to arbitrary multi-dimensional data, consider= ing its +structure.") + (license license:expat))) + +(define-public r-shinybusy + (package + (name "r-shinybusy") + (version "0.3.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinybusy" version)) + (sha256 + (base32 "1bjfi5xdidj8n84mylghvrncvcyg625kj8pnizl59m649k3n10v2")))) + (properties `((upstream-name . "shinybusy"))) + (build-system r-build-system) + (propagated-inputs (list r-htmltools r-htmlwidgets r-jsonlite r-shiny)= ) + (native-inputs (list esbuild r-knitr)) + (home-page "https://github.com/dreamRs/shinybusy") + (synopsis "Busy Indicators and Notifications for 'Shiny' Applications"= ) + (description + "Add indicators (spinner, progress bar, gif) in your shiny applicatio= ns to show +the user that the server is busy. And other tools to let your users know +something is happening (send notifications, reports, ...).") + (license license:gpl3))) + +(define-public r-shinydashboardplus + (package + (name "r-shinydashboardplus") + (version "2.0.3") + (source (origin + (method url-fetch) + (uri (cran-uri "shinydashboardPlus" version)) + (sha256 + (base32 + "10sdb1vddx2ij867pqijr63l4233hw1vnn7mzbs0z23g77x8ra29")) + (modules '((guix build utils))) + (snippet + `(begin + (with-directory-excursion + ,(string-append "inst/shinydashboardPlus-" version + "/js/") + (for-each delete-file + '("app.min.js" + "shinydashboardPlus.min.js" + "shinydashboardPlus.min.js.map"))) + (with-directory-excursion "inst/materialDesign-1.0/js" + (for-each delete-file + '("material.min.js" + "ripples.min.js"))))))) + (properties `((upstream-name . "shinydashboardPlus"))) + (build-system r-build-system) + (arguments + (list + #:tests? #false + #:modules + '((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules + `(,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + #~(modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion + (string-append "inst/shinydashboardPlus-" #$version "/js= /") + (for-each + (match-lambda + ((source . target) + (minify source #:target target))) + `(("app.js" . "app.min.js") + ("shinydashboardPlus.js" . "shinydashboardPlus.min.js") + (,(search-input-file inputs "/dist/js/material.js") + . "materialDesign-1.0/js/material.min.js") + (,(search-input-file inputs "/dist/js/ripples.js") + . "materialDesign-1.0/js/ripples.min.js"))))))))) + (propagated-inputs + (list r-fresh + r-htmltools + r-lifecycle + r-shiny + r-shinydashboard + r-waiter)) + (native-inputs + (list esbuild + r-knitr + (let ((commit "92a2284b47aed56a9d7ae92cf9b40072d27982b3")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DucThanhNguyen/MaterialAdmin= LTE") + (commit commit))) + (file-name (git-file-name "MaterialAdminLTE" + (git-version "0" "0" commit))) + (sha256 + (base32 + "0cn11hxpf25h7xj2lk473z24swgz979dz255zwk2m2fj00iljkn9")))= ))) + (home-page "https://github.com/RinteRface/shinydashboardPlus") + (synopsis "Add more AdminLTE2 components to shinydashboard") + (description + "This package extends shinydashboard with AdminLTE2 components. +AdminLTE2 is a Bootstrap 3 dashboard template. Customize boxes, add timel= ines +and a lot more.") + (license license:gpl2+))) + +(define-public r-shinywidgets + (package + (name "r-shinywidgets") + (version "0.8.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "shinyWidgets" version)) + (sha256 + (base32 "02z8fwvnmi6lacqi6ryxssm1w3mh4vfphjrp3v1d6dij3s3l6z0q")))) + (properties `((upstream-name . "shinyWidgets"))) + (build-system r-build-system) + (propagated-inputs + (list r-anytime + r-bslib + r-htmltools + r-jsonlite + r-rlang + r-sass + r-shiny)) + (home-page "https://github.com/dreamRs/shinyWidgets") + (synopsis "Custom inputs widgets for Shiny") + (description + "This package provides a collection of custom input controls and user +interface components for Shiny applications.") + (license license:gpl3))) + +(define-public r-slanter + (package + (name "r-slanter") + (version "0.2-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "slanter" version)) + (sha256 + (base32 "024dkman0r5qzc215gw0ds932vdaz8krrhv64fjw9pni37ixc3mf")))) + (properties `((upstream-name . "slanter"))) + (build-system r-build-system) + (propagated-inputs (list r-matrix r-pheatmap r-pracma)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=3Dslanter") + (synopsis "Slanted Matrices and Ordered Clustering") + (description + "Slanted matrices and ordered clustering for better visualization of = similarity +data.") + (license license:expat))) + +(define-public r-tglkmeans + (package + (name "r-tglkmeans") + (version "0.5.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "tglkmeans" version)) + (sha256 + (base32 "1plg03k9r4sp8ck5qcj8shblr8378bynyyc7yqwcqv856vkl9icd")))) + (properties `((upstream-name . "tglkmeans"))) + (build-system r-build-system) + (propagated-inputs (list r-cli + r-dofuture + r-dplyr + r-future + r-ggplot2 + r-magrittr + r-matrix + r-metacell + r-plyr + r-purrr + r-rcpp + r-rcppparallel + r-tgstat + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://tanaylab.github.io/tglkmeans/") + (synopsis "Efficient Implementation of K-Means++ Algorithm") + (description + "Efficient implementation of K-Means++ algorithm. For more informati= on see (1) +\"kmeans++ the advantages of the k-means++ algorithm\" by David Arthur and= Sergei +Vassilvitskii (2007), Proceedings of the eighteenth annual ACM-SIAM sympos= ium on +Discrete algorithms, Society for Industrial and Applied Mathematics, +Philadelphia, PA, USA, pp. 1027-1035, and (2) \"The Effectiveness of Lloy= d-Type +Methods for the k-Means Problem\" by Rafail Ostrovsky, Yuval Rabani, Leona= rd J. +Schulman and Chaitanya Swamy .") + (license license:expat))) + +(define-public r-waiter + (package + (name "r-waiter") + (version "0.2.5") + (source (origin + (method url-fetch) + (uri (cran-uri "waiter" version)) + (sha256 + (base32 + "0ya92qr25ssfkzn888b7rr8rn0304f3gz4h4pnc2a95rknbmxhls")))) + (properties `((upstream-name . "waiter"))) + (build-system r-build-system) + (propagated-inputs (list r-htmltools r-r6 r-shiny)) + (native-inputs (list r-knitr)) + (home-page "https://waiter.john-coene.com/") + (synopsis "Loading screen for Shiny") + (description + "This package provides full screen and partial loading screens +for Shiny with spinners, progress bars, and notifications.") + (license license:expat))) + (define-public r-archr (let ((commit "c61b0645d1482f80dcc24e25fbd915128c1b2500") (revision "1")) --=20 2.41.0 From debbugs-submit-bounces@debbugs.gnu.org Wed May 22 13:44:22 2024 Received: (at 71031-done) by debbugs.gnu.org; 22 May 2024 17:44:22 +0000 Received: from localhost ([127.0.0.1]:57258 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s9q0k-0005cx-6Z for submit@debbugs.gnu.org; Wed, 22 May 2024 13:44:22 -0400 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21882) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s9q0h-0005cr-8d for 71031-done@debbugs.gnu.org; Wed, 22 May 2024 13:44:20 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1716399850; cv=none; d=zohomail.com; s=zohoarc; b=THOwTLF0OB3yUk0p80LlsChvpF+BHkTmsA1GnQ8zqcQrXm/mqqiGi4kIcNU5qBsxiZlVLL6WNEbecT2qGtGXOWhwIbRj/NbGA6tZF/g+i6d9bQKubtMAVz4LDX9lAMvdLsHu1/a2Z/z4D5ACL9fORntgbV4Emz2nlm3hpK0wEKU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1716399850; h=Content-Type:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=AJ8lMKKXmzww2rLM36OR9nGRwzTs3gaVMwAb3VXom7s=; b=ZEuphCaaC8mEzswGe4F9LdjWgKx52pmolUBh5f3UC8dQKMAExLmcn/kAHULusuEiROB2VNQtrKvTrsg7zqYYX/57cRwA/ZwrB2N/cVqi5PIAFf4L7kHpzVkVXBcSgBosWThYd0cJAy4kXq+qkkSmItN9wWdEVZVGa7nrPXQ7qtI= 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=1716399850; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:In-Reply-To:References:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=AJ8lMKKXmzww2rLM36OR9nGRwzTs3gaVMwAb3VXom7s=; b=BZw5mvyZot1DkzH6u8UoVjUj87+pUyUK5dMLn298drsZU6h3rwmpg7cjEfJYoGaH 5LGVtzSfe/Ig0xHhcbsbjb7BtQE0IHTM74HsxBvPrsgCD7IEMA91aT1KN2pbt9QKFdz Q2WzFuvauGE1u959wvWhR1Zd9Q8NS8gyPJytI4lg= Received: by mx.zohomail.com with SMTPS id 1716399849180363.99104225016686; Wed, 22 May 2024 10:44:09 -0700 (PDT) From: Ricardo Wurmus To: guix@mawumag.com Subject: Re: [PATCH] Added r-mcview In-Reply-To: <171601865003.8.3299177765362446936.333610631@mawumag.com> (guix@mawumag.com's message of "Sat, 18 May 2024 07:50:46 +0000") References: <171601865003.8.3299177765362446936.333610631@mawumag.com> User-Agent: mu4e 1.12.4; emacs 29.3 Date: Wed, 22 May 2024 19:44:06 +0200 Message-ID: <874japoi6x.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 71031-done Cc: 71031-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 (-) Thank you for this excellent first contribution! This one is a little tricky: mcview depends on r-waiter and r-shinywidgets, both of which bundle a lot of minified JavaScript from unknown sources. Today I finished packaging r-waiter by replacing its use of webpack with esbuild (for which we do have a usable package). This required modification of the esbuild package, which I did in a variant "esbuild-node" to build and install the nodejs libraries. Alas, I wasn't able to do the same for r-shinywidgets. This package still lives in Guix Science for this reason. I split your patch into several commits, one for each package. Those packages that depend on things that are in Guix Science have been moved there. This includes r-mcview itself. Everything else is now in Guix proper. I've moved packages from bioinformatics.scm to cran.scm where appropriate (arranged roughly in alphabetic order). Thanks again for this contribution and welcome to Guix! -- Ricardo From unknown Mon Aug 18 14:24:10 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, 20 Jun 2024 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