diff --git a/.Rbuildignore b/.Rbuildignore index 5e4a3338..0613275f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,4 @@ +^renv$ +^renv\.lock$ ^LICENSE\.md$ ^\.github$ diff --git a/.Rprofile b/.Rprofile index 0547dcc9..f2720dcd 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,3 +1,4 @@ +source("renv/activate.R") if (file.exists('~/.Rprofile')) sys.source('~/.Rprofile', envir = environment()) with_def <- (function() { diff --git a/.github/workflows/bookdown-test.yaml b/.github/workflows/bookdown-test.yaml index 5aba1710..fd9df0e4 100644 --- a/.github/workflows/bookdown-test.yaml +++ b/.github/workflows/bookdown-test.yaml @@ -8,7 +8,7 @@ on: - main - master -name: preview bookdown +name: Preview website jobs: build: @@ -16,15 +16,37 @@ jobs: runs-on: ubuntu-latest container: inseefrlab/utilitr:latest steps: - - name: Checkout Repository - if: ${{ github.repository == 'inseefrlab/utilitr' }} - env: - GITHUB_PAT: ${{ secrets.PAT }} - uses: actions/checkout@master - - name: Install Dependencies - if: ${{ github.repository == 'inseefrlab/utilitr' }} + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + ref: ${{ github.event.pull_request.head.ref }} + repository: ${{github.event.pull_request.head.repo.full_name}} + - name: Configure safe repository + run: | + git config --global --add safe.directory /__w/utilitR/utilitR + - name: Set RENV_PATHS_ROOT + shell: bash run: | - Rscript -e "install.packages(c('remotes', 'htmltools', 'sf'))" + echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV + - name: Install and activate renv + run: | + install.packages("yaml") + install.packages("renv") + renv::status() + renv::activate() + shell: Rscript {0} + - name: Get R and OS version + id: get-version + run: | + cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "") + cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "") + shell: Rscript {0} + - name: Restore Renv package cache + uses: actions/cache@v4 + with: + path: ${{ env.RENV_PATHS_ROOT }} + key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }} + restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}- env: GITHUB_PAT: ${{ secrets.PAT }} - name: Render Book diff --git a/.github/workflows/prod.yaml b/.github/workflows/prod.yaml index 49c32c5a..6b682c62 100644 --- a/.github/workflows/prod.yaml +++ b/.github/workflows/prod.yaml @@ -1,82 +1,42 @@ -name: Production de la documentation - - on: + workflow_dispatch: push: - branches: - - main - - master - - test + branches: renv + +name: Quarto Publish jobs: - docker: - if: "!contains(github.event.commits[0].message, '[skip ci]')" + build-deploy: runs-on: ubuntu-latest + permissions: + contents: write steps: - - - name: Checkout - uses: actions/checkout@v2 - - - name: Set up QEMU - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/setup-qemu-action@v1 - - - name: Set up Docker Buildx - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/setup-buildx-action@v1 - - - name: Login to DockerHub - if: ${{ github.repository == 'inseefrlab/utilitr' }} - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - - name: Build and push - if: ${{ github.repository == 'inseefrlab/utilitr' }} - id: docker_build - uses: docker/build-push-action@v2 - env: - GITHUB_PAT: ${{ secrets.PAT }} - with: - push: true - context: . - tags: | - inseefrlab/utilitr:latest - inseefrlab/utilitr:0.9.1 - - - name: Image digest - run: echo ${{ steps.docker_build.outputs.digest }} - website: - name: Render website - if: "!contains(github.event.commits[0].message, '[skip ci]')" - needs: docker - runs-on: ubuntu-latest - container: inseefrlab/utilitr:latest - steps: - - uses: actions/checkout@v4 + - name: Check out repository + uses: actions/checkout@v4 + + - name: Install R + uses: r-lib/actions/setup-r@v2 with: - fetch-depth: 0 - ref: ${{ github.event.pull_request.head.ref }} - repository: ${{github.event.pull_request.head.repo.full_name}} + r-version: '4.4.1' + - name: Install dependencies run: | - git config --global --add safe.directory /__w/utilitR/utilitR - Rscript -e "install.packages(c('remotes'))" - Rscript -e "remotes::install_github('rstudio/htmltools')" - Rscript -e "remotes::install_github('r-spatial/sf', dependencies = TRUE)" - env: - GITHUB_PAT: ${{ secrets.PAT }} - - name: Render Book - run: | - ls - git remote -v - git config --global user.email quarto-github-actions-publish@example.com - git config --global user.name "Quarto GHA Workflow Runner" - quarto render --to html - quarto publish gh-pages --no-render --no-browser - - uses: actions/upload-artifact@v2 + sudo ./docker/dependencies.sh + rm -rf renv/ + rm .Rprofile + Rscript -e "install.packages('yaml')" + + - name: Install renv packages + uses: r-lib/actions/setup-renv@v2 with: - name: _public - path: _public/ - retention-days: 5 + cache-version: 2 + + - name: Set up Quarto environment + uses: quarto-dev/quarto-actions/setup@v2 + + - name: Render and Publish + uses: quarto-dev/quarto-actions/publish@v2 + with: + target: gh-pages + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/01_R_Insee/Fiche_installer_packages.qmd b/01_R_Insee/Fiche_installer_packages.qmd index 04434162..fdf11dd9 100644 --- a/01_R_Insee/Fiche_installer_packages.qmd +++ b/01_R_Insee/Fiche_installer_packages.qmd @@ -122,7 +122,7 @@ contiendra les modifications les plus récentes. Installer depuis une forge permet ainsi de récupérer la version de développement d'un _package_ (seules les versions stables sont en général disponibles sur le CRAN). Pour installer un _package_ tel qu'il était à un moment donné, il est également possible de -faire suivre le nom du dépôt par une référence à un `r with_def("commit")`, à un _tag_ (une version) ou à une `r with_def("branche")`. Voici un exemple avec un _tag_ : `remotes::install_gitlab("py_b/funprog@v-0.3.0")`. Voici un exemple avec un commit : `remotes::install_github("InseeFrLab/doremifasolData@a9df2d3d0e372")`. +faire suivre le nom du dépôt par une référence à un `commit`, à un _tag_ (une version) ou à une ` branche`. Voici un exemple avec un _tag_ : `remotes::install_gitlab("py_b/funprog@v-0.3.0")`. Voici un exemple avec un commit : `remotes::install_github("InseeFrLab/doremifasolData@a9df2d3d0e372")`. ::: {.callout-note} Lorsque vous installez un _package_ depuis une forge logicielle, `R` crée automatiquement une archive temporaire (un fichier `.tar.gz`), puis installe le _package_ à partir de celle-ci. Si vous travaillez dans un environnement Windows, il est nécessaire que `Rtools` soit installé sur votre poste pour que `R` puisse construire l'archive. diff --git a/01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd b/01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd deleted file mode 100644 index 576d5721..00000000 --- a/01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd +++ /dev/null @@ -1,384 +0,0 @@ -# Utiliser `RStudio` sur l'environnement SSP Cloud {#sspcloud} - -::: {.callout-important} -## Tâche concernée et recommandation - -Vous pouvez utiliser `R` et RStudio sur le SSP Cloud pour mener des expérimentations qui seraient difficiles à réaliser dans AUS. En revanche, le SSP Cloud ne doit pas être utilisé pour réaliser des tâches de production statistique, ni pour traiter des données confidentielles. -::: - -::: {.callout-note} -Certains exemples de cette fiche utilisent les données disponibles dans le _package_ `doremifasolData` ; vous ne pourrez reproduire ces exemples que si ce _package_ est installé sur la machine sur laquelle vous travaillez. Si vous ne savez pas si ce _package_ est déjà installé, consultez la fiche [Comment utiliser la documentation `utilitR`](#presentation-utilitr). -::: - -## Présentation succincte du SSP Cloud - -**Le SSP Cloud est une plate-forme informatique hébergée à l'Insee et ouverte à tous les agents de la statistique publique.** Elle permet aux statisticiens d'utiliser un grand nombre de logiciels de _data science_ (`R`, `Python`, `PostgreSQL`, `Jupyter`, `Spark`, `Tensorflow`...) dans un environnement informatique ergonomique et performant. Il faut donc noter que le SSP Cloud n'est donc pas spécifiquement conçu pour utiliser `R`. - -**Le SSP Cloud est une plate-forme sur laquelle vous pouvez mener des expérimentations qui seraient difficiles à réaliser dans AUS**, soit parce qu'AUS ne propose pas le logiciel dont vous avez besoin, soit parce que votre traitement demande des ressources informatiques particulièrement importantes. - -En revanche, **le SSP Cloud n'est pas une infrastructure de production, et n'offre donc pas les mêmes garanties de service qu'AUS**. De plus, le traitement de données confidentielles sur le SSP Cloud n'est pas autorisé par défaut. - - -## Comment travailler avec un service RStudio sur le SSP Cloud - -### Créer un compte sur le SSP Cloud - -Il est nécessaire de disposer d'un compte personnel **SSP Cloud** pour en utiliser les services. Si vous n'avez pas de compte sur le **SSP Cloud**, vous pouvez vous en créer un en [cliquant sur ce lien (https://datalab.sspcloud.fr/home)](https://datalab.sspcloud.fr/home) puis suivre les indications. Deux points sont importants à noter : - -- vous devez utiliser votre adresse mail professionnelle (de l'Insee ou de votre SSM) ; -- **votre nom d'utilisateur ne doit contenir ni caractères accentués, ni caractère spécial, ni signe de ponctuation**. Ce point est essentiel, car votre compte ne fonctionnera pas si votre nom d'utilisateur comprend l'un de ces caractères. Pour les agents de l'Insee, le plus simple est de choisir votre IDEP puisqu'il respecte ces règles. Pour les agents des SSM ne disposant pas d'IDEP, vous pouvez adopter le format `prenomnom` en faisant attention aux règles précédentes. Par exemple, si vous vous appelez Jérôme-Gérard L'Hâltère, votre nom d'utilisateur pourra être `jeromegerardlhaltere`. - -::: {.callout-note} -La grande majorité des problèmes rencontrés à la création d'un compte SSP Cloud découle d'un `username` ne respectant pas ces règles. Dans ce cas, la seule solution consiste à demander aux administrateurs du SSP Cloud de supprimer votre compte, pour que vous puissiez en créer un nouveau. Vous pouvez contacter les administrateurs en écrivant un message sur le [salon Tchap `SSPCloud`](https://www.tchap.gouv.fr/#/room/#SSPCloudXDpAw6v:agent.finances.tchap.gouv.fr). -::: - -### Changer la langue du SSP Cloud - -Par défaut, l'interface du SSP Cloud est en anglais. Pour choisir le français, deux solutions sont offertes : - -- Cliquer en bas à droite de la fenêtre puis choisir le français dans les options proposées. - -![](../pics/SSPCloud/00_choisir_langue.png){fig-alt="Lancer un service RStudio"} - -- Cliquer sur `My account` dans le menu de gauche puis dans l'onglet `Interface preferences` vous pouvez changer la langue dans la fenêtre qui s'affiche. - -### Créer un service RStudio - -Voici comment procéder pour créer un service RStudio (avec l'interface en français) : - -- [Cliquer sur l'onglet **"Catalogue de services"**](https://datalab.sspcloud.fr/my-lab/catalogue) qui est accessible à gauche grâce au symbole - -![](../pics/SSPCloud/inline_pics/01_bouton_services.png){width="30px"} - -- La fenêtre suivante s'affiche (pour y accéder directement, -[suivre ce lien](https://datalab.sspcloud.fr/catalog/inseefrlab-helm-charts-datascience)). - - -![](../pics/SSPCloud/01_catalogue_services.png) - - -- RStudio est à la une. Cliquer sur le bouton `LANCER` ; -- La page suivante s'ouvre : - -![](../pics/SSPCloud/02_lancer_rstudio.png){fig-alt="Lancer un service RStudio"} - -- Dans la page qui s'affiche, vous pouvez définir les options de votre service RStudio (voir la section [Définir les options d'un service RStudio](#options-rstudio)). -Vous pouvez lancer le service en cliquant sur **Lancer**. - - -![](../pics/SSPCloud/02b_lancer_rstudio_options.png){fig-alt="Page de création d'un service RStudio"} - - - - -### Accéder à ses services - -Pour accéder à l'ensemble de ses services, il est nécessaire de cliquer sur le bouton -```{r bouton_mes_services, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/03_bouton_mes_services.png", compression = FALSE) -``` -\ . La page qui s'ouvre permet alors de lister l'ensemble des services ouverts : - -```{r, echo = FALSE, fig.cap= "Liste des services ouverts", out.width = "100%"} -utilitr::include_image("../pics/SSPCloud/03_liste_services.png", ratio_compression = 1) -``` - -Pour accéder à l'un d'eux il faut cliquer sur le bouton - -![](../pics/SSPCloud/inline_pics/Se_connecter_service.png){width="60px"} - -Il est recommandé de ne pas garder actifs des services qui ne sont plus utiles. -Au coût environnemental d'avoir des ressources allouées inactives, s'ajoute -le fait que cela mobilise des ressources qui pourraient être utilisées -par d'autres. La procédure pour fermer des services est décrite plus bas. - - -### Se connecter à un service RStudio - -Une fois que votre service RStudio est créé, il faut vous connecter à ce service. -Pour ce faire, il faut vous identifier avec un nom d'utilisateur -et un mot de passe (différent de celui de votre compte SSP Cloud). -Pour récupérer ce mot de passe, il y a deux façons de faire. Vous pouvez cliquer sur `README` et copier le mot de passe, ou cliquer sur la clé -```{r key_button, out.extra='style="display: inline-block; padding: 0; width: 120px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/key.png", compression = FALSE) -``` -\ présente dans la page -*Mes services* -```{r, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/03_bouton_mes_services.png", compression = FALSE) -``` -\ . Cette action permet de copier le mot de passe dans le presse-papier ce qui -facilite son utilisation. - -Pour accéder à un service, le bouton -```{r, out.extra='style="display: inline-block; padding: 0; width: 60px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/Se_connecter_service.png", compression = FALSE) -``` -\ permet d'ouvrir une page d'authentification. - -```{r 99_SSPCloud_4bis, echo = FALSE, out.width = "80%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_4bis.png", ratio_compression = 1) -``` - -Les identifiants sont : - -- `Username` : `rstudio` ; -- `Password` : le _password_ copié précédemment (il suffit de faire `Ctrl + V`). - -```{r 99_SSPCloud_5bis, echo = FALSE, out.width = "50%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_5bis.png", ratio_compression = 1) -``` - -L'interface habituelle de RStudio s'affiche alors dans la fenêtre. - -```{r 99_SSPCloud_6, echo = FALSE, out.width = "80%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_6.png", ratio_compression = 1) -``` - -## Définir les options d'un service RStudio {#options-rstudio} - -Lors de la création de votre service RStudio, vous pouvez définir les options du service en naviguant dans les différents onglets de l'interface du SSP Cloud (cadre rouge). - -```{r, echo = FALSE, out.width = "100%"} -utilitr::include_image("../pics/SSPCloud/99_SSPCloud_3bis.png", ratio_compression = 1) -``` - -Les principales options sont les suivantes : - -- L'**option `memory`** (dans l'onglet `Resources`) définit la quantité minimum garantie de mémoire vive (mesurée en Mo) que votre service RStudio peut utiliser. **Cette option est particulièrement importante** et vous devez choisir soigneusement sa valeur : si vos traitements requièrent plus de mémoire que la valeur de `mem`, la seule solution consiste à lancer un autre service RStudio avec une valeur de `mem` plus élevée. Il est conseillé d'utiliser 10000 comme valeur par défaut. -- L'**option `cpu`** (dans l'onglet `Resources`) définit le nombre minimal de processeurs alloués à votre service RStudio, c'est un minimum garanti. Il est conseillé d'utiliser 2 comme valeur par défaut si vos traitements nécessitent de la parallélisation et laisser l'option par défaut sinon. -- L'**option `Enable IP protection`** (dans l'onglet `Security`) est une option de sécurité informatique assez contraignante, qui est activée par défaut. Il est conseillé de la laisser activée. Toutefois, vous pouvez éventuellement la désactiver, notamment si vous savez que vous allez devoir accéder à l'environnement RStudio depuis des adresses IP différentes (exemple : au bureau puis en télétravail). -- L'**option `version`** (dans l'onglet `Service`) détermine l'environnement dans lequel RStudio va s'ouvrir. Il s'agit d'un environnement contenant une version donnée de `R` ainsi que des packages pré-installés. Par exemple, l'image `utilitR` disponible propose l'ensemble des dépendances (elles sont nombreuses...) nécessaires pour reproduire tous les exemples présents dans cette documentation. -- L'**option `PersonalInit`** (dans l'onglet `Init`) permet de référencer un script d'initialisation qui exécutera une série d'actions prédéfinies avant de lancer le service, par exemple copier localement des données, lancer un projet RStudio ou définir des paramètres d'affichage de l'interface. Un exemple d'un tel fichier Init utilisé pour des formations peut être trouvé [ici](https://github.com/InseeFrLab/formation-r-lissage-spatial/blob/f3258469513cabd2de328dc92165641f8f452bca/utils/init.sh). C'est l'URL du fichier sur github.com qui doit être référencé, **dans sa version *Raw*** (afficher le fichier dans Github et cliquer sur `Raw` en haut à droite pour obtenir cette URL). - -::: {.callout-note} -**Les options d'un service RStudio ne peuvent être définies qu'au moment de la création du service.** Si vous vous rendez compte qu'une option du service ne convient pas au traitement que vous voulez faire, vous devez supprimer votre service RStudio et en lancer un nouveau avec les bonnes options. Lorsqu'un ensemble d'options vous conviennent, il est possible de l'enregistrer pour les retrouver lors du prochain lancement d'un service. Pour cela, cliquez sur l'icône de marque-page en haut à droite du panneau de paramétrage. La liste des configurations ainsi définies comme favorites apparaîtront dans SSP Cloud dans la rubrique `Mes services`, dans la colonne `Enregistrés`. -::: - -### Utiliser Github et Gitlab sur le SSP Cloud - -Les services ouverts sur le SSPCloud ont une durée de vie limitée. -Pour conserver les codes afin de pouvoir les réutiliser ultérieurement ou les -rendre disponibles à d'autres personnes, il est nécessaire d'utiliser une -plateforme type Gitlab et Github. - -Dans le catalogue des services, une plateforme Gitlab est disponible. -Son adresse est (c'est un [`Service partagé`](https://datalab.sspcloud.fr/services)). Cependant, elle n'apporte pas un niveau de sécurité -supérieur aux plateformes ou -. Il est donc recommandé de privilégier l'une de -ces deux plateformes plutôt que le `Gitlab` mis à disposition sur le -SSPCloud. - -Le SSPCloud ne permet qu'une authentification HTTPS. L'authentification SSH -est donc désactivée -(voir la fiche [Configurer `Git` sur son poste de travail](#git-config) pour plus -de détails). Les fonctionnalités standards de RStudio pour favoriser l'usage -de Git sont disponibles (voir la fiche [Utiliser `Git` avec RStudio](#git) pour plus -de détails). - - -### Supprimer un service RStudio - -Les services RStudio peuvent être arrêtés à tout moment. Avant d'arrêter un service -RStudio, il est recommandé de s'assurer que les codes (via Gitlab ou autre Forge utilisant Git, voir ci-dessus) -et les données (via S3, voir ci-dessous) à conserver ont bien été -sauvegardés. - -```{r 04_exemple_service, echo = FALSE, fig.cap= "Accéder aux options d'un service", out.width = "35%"} -utilitr::include_image("../pics/SSPCloud/04_exemple_service.png", ratio_compression = 1) -``` - -Pour supprimer un service, il faut se servir de l'un des trois boutons qui permettent d'accéder aux options d'un service RStudio (cadre rouge) : - -* Le bouton de gauche permet d'obtenir des informations sur la configuration de votre service (notamment pour l'accès au système de stockage S3) ; -* Le bouton du milieu permet de tuer définitivement un service qui disparaîtra -du tableau des services ouverts ; -* Le dernier de droite d'accéder à *Graphana*, un outil qui permet de -suivre en temps réel l'usage mémoire et CPU d'un service RStudio. C'est utile pour bien comprendre ce que fait votre service RStudio. - -## Utiliser des données stockées sur le système de stockage S3 - -### Pourquoi utiliser S3 sur le SSP Cloud ? - -Le SSP Cloud propose des environnements (comme les services ` RStudio`, `Jupyter`, etc.) pour exécuter des programmes informatiques. Ces environnements sont **temporaires par définition** (quelques heures ou quelques jours), et ne peuvent donc pas servir à stocker des données ou des programmes informatiques. Cela a pour conséquence que les programmes informatiques et les données doivent être stockés dans d'autres espaces : - -* *stockage des codes* : il est nécessaire d'utiliser une plate-forme de développement pour stocker des programmes informatiques, telles que [Gitlab](www.gitlab.com) ou [Github](www.github.com). -* *stockage des données* : la plateforme SSP Cloud propose un système de stockage de données nommé S3. Depuis votre service RStudio, vous pourrez facilement accéder à des données stockées sur S3 grâce au _package_ `aws.s3`. - -::: {.callout-note} -Voici deux règles à respecter pour faire un bon usage de ces deux espaces de stockage : - -* Les plate-formes telles que Gitlab ou Github ne doivent **jamais** être utilisées pour stocker des données (uniquement des codes). -* Le système de stockage S3 ne doit **jamais** être utilisé pour stocker des données confidentielles. -::: - -### Qu'est-ce que le système de stockage S3 ? - -Le système S3 (*Simple Storage System*) est un système de stockage développé par Amazon et qui est maintenant devenu une référence pour le stockage en ligne. Il s'agit d'une architecture à la fois sécurisée (données cryptées, accès restreints) et performante. - -Le concept central du système S3 est le *bucket*. Un *bucket* est un espace (privé ou partagé) où on peut stocker une arborescence de fichiers. Pour accéder aux fichiers figurant dans un *bucket* privé, il faut fournir des jetons d'accès (l'équivalent d'un mot de passe) reconnus par le serveur de stockage. On peut alors lire et écrire dans le *bucket*. - -### Explorer son dépôt de fichiers - -Il est possible d'utiliser l'interface du `SSP Cloud` pour explorer les fichiers présents dans S3 ainsi qu'ajouter ou télécharger manuellement des fichiers. Le raccourci pour accéder aux fichiers disponibles se trouve dans la barre latérale *Mes fichiers* -```{r onyxia_files, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/onyxia_files.png", compression = FALSE) -``` -\ . En cliquant sur cette icône, on ouvre un explorateur qui permet de visualiser les fichiers présents sur son *bucket* personnel : - -```{r onyxia_files2, echo = FALSE, out.width = "100%"} -utilitr::include_image("../pics/SSPCloud/minio/onyxia_files2.png", ratio_compression = 1) -``` - -Il est possible de naviguer dans l'arborescence depuis cette fenêtre afin, par exemple, de récupérer un chemin qu'on va utiliser avec `R`. La vignette verte sur la droite indique la commande à utiliser dans un terminal pour lister les fichiers du répertoire courant. Elle permet donc notamment de connaître le chemin d'accès à un fichier permettant d'y accéder à travers un service RStudio du SSP Cloud. - -Par défaut, le *bucket* utilisateur créé à l'inscription sur le SSP Cloud est vierge. Il est néanmoins utile de créer directement un dossier particulier, nommé "diffusion". Grâce à une politique de droits spécifique, ce dossier et son contenu sont accessibles (en lecture) à tous les utilisateurs du SSP Cloud. Il est donc à privilégier pour déposer des fichiers destinés à être diffusés, comme des données partagées ou des supports de formation. - -### Utiliser S3 avec un service RStudio - -**Lorsqu'on crée un service RStudio sur le SSP Cloud, des droits d'accès temporaires au système S3 sont automatiquement initialisés.** Ces droits permettent de communiquer avec le serveur de stockage, mais leur usage est complexe. Heureusement, il existe le _package_ `aws.s3` qui simplifie beaucoup les interactions entre le service RStudio et S3 en proposant des fonctions de lecture et d'écriture similaires à celles existantes pour lire ou écrire un fichier depuis un poste personnel. - -#### Vérifier les droits d'accès à un *bucket* - -**Pour lister l'ensemble des fichiers disponibles dans un _bucket_, il suffit de charger le _package_ `aws.s3` et d'exécuter la commande `get_bucket()`.** Cette commande donne quelques informations sur les fichiers stockés dans le _bucket_ : nom et emplacement, taille et date de dernière modification. Il n'est pas nécessaire de configurer les droits d'accès au système S3, car le service RStudio en dispose dès son lancement. - -Imaginons qu'on souhaite accéder au _bucket_ nommé `donnees-insee` qui contient des fichiers d'exemples ([lien](https://datalab.sspcloud.fr/my-files/donnees-insee)) et auquel tout utilisateur du SSP-Cloud a accès. Voici comment afficher la liste des objets contenus dans ce _bucket_ : - -```{r, eval = FALSE} -# Attention cet exemple renvoie un très grand nombre de résultats -# library(aws.s3) -aws.s3::get_bucket("donnees-insee", region = "") -``` - -::: {.callout-tip} -La commande `get_bucket()` peut renvoyer un grand nombre de résultats si le _bucket_ contient un grand nombre de fichiers. Le _bucket_ `donnees-insee` contient ainsi plus de 1000 fichiers. Il est donc conseillé d'utiliser l'option `prefix` pour restreindre le chemin des fichiers que l'on souhaite lister. Par exemple, le code suivant fournit la liste des fichiers situés dans le répertoire `diffusion/ESTEL/2015` du _bucket_ `donnees.insee` : - -```{r, eval = FALSE} -#library(aws.s3) -aws.s3::get_bucket("donnees-insee", region = "", prefix = "diffusion/ESTEL/2015") -``` -::: - -#### Renouveler des droits d'accès périmés - -**Les droits d'accès au S3 sont temporaires par définition et sont donc rapidement périmés.** Si vous utilisez un service RStudio pendant plusieurs jours, il est probable que `R` renverra l'erreur suivante : - -```{text} -$ Code : chr "InvalidAccessKeyId" -$ Message : chr "The Access Key Id you provided does not exist in our records." -$ BucketName : chr "donnees-insee" -$ Resource : chr "/donnees-insee/" -[... lignes coupées ...] -Error in parse_aws_s3_response(r, Sig, verbose = verbose) : - Forbidden (HTTP 403). -``` - -Voici la procédure à suivre pour renouveler les droits d'accès à S3. Cliquer sur `Mon compte` -```{r, out.extra='style="display: inline-block; padding: 0; width: 30px;"', echo = FALSE} -utilitr::include_image("../pics/SSPCloud/inline_pics/moncompte.png", compression = FALSE) -``` - -Cliquer sur l'onglet `Connexion au stockage`. -La première ligne vous indique jusqu'à quand les droits d'accès sont valides. Vérifier que les droits d'accès sont bien formatés pour `R` (cadre rouge), puis copier les droits d'accès (cadre bleu). - -```{r, echo = FALSE, out.width = "70%"} -utilitr::include_image("../pics/SSPCloud/jetons_onyxia.png", ratio_compression = 1) -``` - - - -Coller les droits d'accès dans un script `R` de votre service RStudio, puis exécuter les lignes de code sélectionnées dans la capture d'écran ci-dessous. Le bouton dans le cadre bleu ci-dessus permet de -copier les commandes qui conviennent dans le presse-papier. La partie la -plus importante est la suivante (en remplaçant `XXXXXXXXXXXXXXXXX` -par les valeurs en question): - -```{r, eval = FALSE} -Sys.setenv("AWS_ACCESS_KEY_ID" = "XXXXXXXXXXXXXXXXX", - "AWS_SECRET_ACCESS_KEY" = "XXXXXXXXXXXXXXXXX", - "AWS_DEFAULT_REGION" = "us-east-1", - "AWS_SESSION_TOKEN" = "XXXXXXXXXXXXXXXXX", - "AWS_S3_ENDPOINT"= "minio.lab.sspcloud.fr") -``` - -Ces variables d'environnement permettent au package `aws.s3` de -déterminer la localisation du système de fichier et l'identité -de la session `R` - - - - -#### Lire les fichiers d'un *bucket* - -**Une fois que l'on connaît l'emplacement d'un objet dans un _bucket_, on peut l'importer dans le service RStudio avec la fonction `s3read_using()`.** Cette fonction permet d'importer n'importe quel objet, mais nécessite que l'on précise la fonction à utiliser pour lire l'objet. Les arguments de `s3read_using()` sont les suivants : - -- `FUN` : la fonction à utiliser pour lire le fichier ; cet argument doit être écrit sous la forme `package::function` ; -- `object` : le chemin du fichier à importer ; -- `bucket` : le _bucket_ dans lequel se trouve l'objet ; -- `opts` : les options. - -Dans l'exemple qui suit, on souhaite importer les données du dispositif Filosofi 2017 agrégées par commune, qui sont stockées dans le chemin `/diffusion/FILOSOFI/2017/FILOSOFI_COM.csv` dans le *bucket* `donnees-insee`. On importe ces données avec la fonction `fread()` du _package_ `data.table`. Vous pouvez consulter la fiche [Importer des fichiers plats (`.csv`, `.tsv`, `.txt`)] pour une présentation détaillée de cette fonction. - -```{r, eval = FALSE} -df <- - aws.s3::s3read_using( - FUN = data.table::fread, - # Mettre les options de FUN ici - object = "/diffusion/FILOSOFI/2016/FILOSOFI_COM.csv", - bucket = "donnees-insee", - opts = list("region" = "") - ) -``` - -Il est possible d'utiliser toutes les options de la fonction d'importation, en les ajoutant immédiatement après l'argument `FUN`. Ainsi, dans l'exemple qui suit, les options `nrows` et `select` de la fonction `fread()` sont utilisées pour importer uniquement les 1000 premières lignes du fichier, et pour sélectionner trois colonnes. - -```{r, eval = FALSE} -df2 <- - aws.s3::s3read_using( - FUN = data.table::fread, - # Les options de fread sont ici - nrows = 1000L, - select = c("CODGEO", "LIBGEO", "TP6016"), - object = "/diffusion/FILOSOFI/2016/FILOSOFI_COM.csv", - bucket = "donnees-insee", - opts = list("region" = "") - ) -``` - - -#### Ecrire un fichier dans un *bucket* - -**La fonction `s3write_using()` permet d'exporter un objet depuis le service RStudio vers un _bucket_, mais nécessite que l'on précise la fonction à utiliser pour écrire l'objet.** Exporter vers un _bucket_ nécessite évidemment d'avoir les droits en écriture sur le _bucket_ concerné. Les arguments de `s3write_using()` sont les suivants : - -- `x` : l'objet à exporter ; -- `FUN` : la fonction à utiliser pour écrire le fichier ; cet argument doit être écrit sous la forme `package::function` ; -- `object` : le chemin du fichier à exporter ; -- `bucket` : le _bucket_ dans lequel l'objet sera exporté ; -- `opts` : les options. - -Comme pour la fonction `s3read_using`, il est possible d'utiliser toutes les options de la fonction d'exportation, en les ajoutant immédiatement après l'argument `FUN`. Dans l'exemple suivant, on charge dans le service RStudio la table du code officiel géographique 2019 disponible dans le _package_ `doremifasolData`, puis on l'exporte en format `csv` dans le fichier `data/cog_com_2019.csv` du _bucket_ `mon_bucket`. On utilise les options `sep` et `col.names` de la fonction `fwrite()` pour définir le séparateur et exporter les noms de colonnes. - -```{r, eval = FALSE} -# Attention, cet exemple n'est pas directement reproductible -# Il faut avoir les droits en écriture sur le bucket -library(doremifasolData) -cog_com_2019 <- doremifasolData::cog_com_2019 - -aws.s3::s3write_using( - cog_com_2019, - FUN = data.table::fwrite, - # Les options de fread sont ici - sep = " ;", - col.names = TRUE, - object = "data/cog_com_2019.csv", - bucket = "mon_bucket", - opts = list("region" = "") -) -``` - - -## Liens utiles - -- Le salon Tchap [SSPCloud](https://www.tchap.gouv.fr/#/room/#SSPCloudXDpAw6v:agent.finances.tchap.gouv.fr) ; -- Le salon Tchap d'assistance aux utilisateurs des **Logiciels Statistiques et Libre Service** [Insee - Outils Stats V2](https://www.tchap.gouv.fr/#/room/#InseeOutilsStatsv2wtxSdth:agent.finances.tchap.gouv.fr) ; -- Un [tutoriel sur le SSP Cloud](https://github.com/RLesur/sspcloud-demo). -- La [documentation en ligne du Datalab](https://docs.sspcloud.fr/) diff --git a/01_R_Insee/Fiche_utiliser_ressources.qmd b/01_R_Insee/Fiche_utiliser_ressources.qmd index c87aaa86..0a38d0e7 100644 --- a/01_R_Insee/Fiche_utiliser_ressources.qmd +++ b/01_R_Insee/Fiche_utiliser_ressources.qmd @@ -79,9 +79,9 @@ clavier suivant : Ctrl + ⇧ Shift + Echap. ::: Lorsque la fenêtre suivante s'affiche, il faut cliquer sur `Plus de détails`. -```{r entree_fiche_tskmngr, echo = FALSE, fig.cap = "Le gestionnaire des tâches Windows", out.width = "50%"} -utilitr::include_image("../pics/utiliser_ressources/TskMngr1small.png", compression = FALSE) -``` +![](/pics/utiliser_ressources/TskMngr1small.png) + + ### Utiliser le gestionnaire des tâches @@ -91,9 +91,7 @@ L'onglet qui vous sera le plus utile est l'onglet `Utilisateurs`. Il affiche la - les lignes du tableau indiquent le taux d'utilisation des processeurs et le taux d'occupation de la mémoire vive, _au niveau de chaque utilisateur_. Vous devez normalement retrouver votre IDEP dans la première colonne (les IDEP sont masqués sur les captures d'écran pour des raisons de sécurité). Le cadre bleu correspond par exemple à l'auteur de cette fiche. Vous pouvez constater qu'il utilise 7,5% des processeurs et qu'il occupe environ 10 Go de mémoire vive. - En cliquant sur la petite flèche grise (indiquée par la flèche noire), vous pouvez afficher la consommation de ressources de chacun des programmes que vous utilisez. -```{r, echo = FALSE, fig.cap= "L'onglet Utilisateurs du gestionnaire des tâches"} -utilitr::include_image("../pics/utiliser_ressources/TskMngr2bis.png", compression = FALSE) -``` +![](/pics/utiliser_ressources/TskMngr2bis.png) Voici trois références à garder en tête pour superviser votre session `R` : @@ -164,13 +162,12 @@ Il y a deux façons de nettoyer la mémoire vive: - Méthode n°1: exécuter `gc()`; - Méthode n°2: utiliser l'interface proposée par RStudio. Il faut cliquer sur la petite flèche rouge, puis sur `Free unused R Memory`. -```{r, echo = FALSE, fig.cap = "Libérer la mémoire inutilisée", out.width = "50%"} -utilitr::include_image("../pics/utiliser_ressources/gc_gui1.png", compression = FALSE) -``` -```{r, echo = FALSE, out.width = "50%"} -utilitr::include_image("../pics/utiliser_ressources/gc_gui2.png", compression = FALSE) -``` +![](/pics/utiliser_ressources/gc_gui1.png) + + +![](/pics/utiliser_ressources/gc_gui2.png) + ::: {.callout-note} Voici deux remarques sur la fonction `gc()` : diff --git a/01_R_Insee/presentation_utilitr.qmd b/01_R_Insee/presentation_utilitr.qmd index 88b1b195..3a5938b3 100644 --- a/01_R_Insee/presentation_utilitr.qmd +++ b/01_R_Insee/presentation_utilitr.qmd @@ -36,12 +36,7 @@ avec `Github`. -```{r} -#| echo: false -#| output: false -#| warning: false -liste_contributeurs <- paste0(paste(format(Filter(function(x) !("cph" %in% x$role), desc::desc_get_authors()), include = c("given", "family")), collapse = ", "), ".") -``` +_to be completed_ Le projet `utilitR` est un projet collaboratif qui a bénéficié des contributions de : `{r} liste_contributeurs` diff --git a/03_Fiches_thematiques/Fiche_configurer_git.qmd b/03_Fiches_thematiques/Fiche_configurer_git.qmd index c21ca1ed..77d0f92e 100644 --- a/03_Fiches_thematiques/Fiche_configurer_git.qmd +++ b/03_Fiches_thematiques/Fiche_configurer_git.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Configurer `Git` sur son poste de travail {#git-config} ## Tâches concernées et recommandations @@ -21,7 +25,7 @@ un _login_ et un mot de passe. ## Les différentes forges utilisables -Une `r with_def("forge")` est un espace informatique en ligne qui accueille des dépôts distants. Un dépôt distant (_remote repository_ en anglais) est un dossier que vous pouvez utiliser pour stocker vos codes (et leur historique), et pour partager des codes avec vos collègues ou stocker vos codes personnels. +Une `forge` est un espace informatique en ligne qui accueille des dépôts distants. Un dépôt distant (_remote repository_ en anglais) est un dossier que vous pouvez utiliser pour stocker vos codes (et leur historique), et pour partager des codes avec vos collègues ou stocker vos codes personnels. Une forge prend généralement forme d'un site internet. Il existe deux forges principales : @@ -40,7 +44,7 @@ Une forge interne `GitLab` est accessible depuis AUS. Son adresse, ainsi que des ::: ::: {.callout-note} -Une instance `GitLab` est disponible sur le SSP Cloud [https://git.lab.sspcloud.fr/] avec laquelle peut interagir un service `RStudio` [lien vers fiche quand elle sera là], et vous pouvez l'utiliser si vous le souhaitez. Toutefois, le SSP Cloud est une plateforme accessible depuis Internet et a donc accès aux dépôts hébergés sur ou . Il est donc conseillé d'utiliser une de ces deux `r with_def("forges")` plutôt que . +Une instance `GitLab` est disponible sur le SSP Cloud [https://git.lab.sspcloud.fr/] avec laquelle peut interagir un service `RStudio` [lien vers fiche quand elle sera là], et vous pouvez l'utiliser si vous le souhaitez. Toutefois, le SSP Cloud est une plateforme accessible depuis Internet et a donc accès aux dépôts hébergés sur ou . Il est donc conseillé d'utiliser une de ces deux `forges` plutôt que . ::: @@ -132,7 +136,7 @@ utilitr::include_image("../pics/config_git/password_conf.png", compression = FAL ``` Une fois le mot de passe configuré, il ne reste plus -qu'à `r with_def("cloner")` le dépôt distant sur lequel on veut travailler, +qu'à `cloner` le dépôt distant sur lequel on veut travailler, par exemple depuis `RStudio`, suivant le protocole décrit dans la fiche [Utiliser Git avec RStudio](#git), en ayant pris soin de sélectionner l'URL correspondant au protocole `HTTPS`, comme ci-dessous : diff --git a/03_Fiches_thematiques/Fiche_git_utilisation.qmd b/03_Fiches_thematiques/Fiche_git_utilisation.qmd index 0c682a37..d80dff0a 100644 --- a/03_Fiches_thematiques/Fiche_git_utilisation.qmd +++ b/03_Fiches_thematiques/Fiche_git_utilisation.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Utiliser `Git` avec RStudio {#git} ## Tâches concernées et recommandations @@ -16,18 +20,18 @@ Il est également souhaitable de lire au préalable la fiche [Configurer Git sur * Ne jamais utiliser `Git` pour sauvegarder les données ; * Utiliser l'interface graphique de `RStudio` pour les usages courants de `Git`, plutôt que la ligne de commande ; -Vous pouvez utiliser `Git` _via_ la ligne de commande si vous le souhaitez. En revanche, il est _très fortement déconseillé_ d'exécuter une commande qui comprendrait les termes `force` ou `r with_def('rebase')`. +Vous pouvez utiliser `Git` _via_ la ligne de commande si vous le souhaitez. En revanche, il est _très fortement déconseillé_ d'exécuter une commande qui comprendrait les termes `force` ou rebase. **Recommandations sur l'initialisation de `Git`** * Il est recommandé d'utiliser `Git` dès le lancement de votre projet, même s'il est possible de commencer à suivre un projet déjà existant avec `Git`. -* Il est recommandé de commencer par créer un dépôt distant sur une forge (`Gitlab`, `Github`...), puis de `r with_def("cloner")` ce dépôt pour travailler sur votre poste local. +* Il est recommandé de commencer par créer un dépôt distant sur une forge (`Gitlab`, `Github`...), puis de clôner ce dépôt pour travailler sur votre poste local. * Il est recommandé de renseigner immédiatement le fichier `.gitignore` afin d'exclure certains fichiers du suivi des modifications (notamment les fichiers de données). **Recommandations sur l'usage des branches** -* Utiliser RStudio pour créer une branche ou naviguer entre les `r with_def("branches")` ; -* Utiliser les interfaces `Github` ou `Gitlab` pour fusionner deux `r with_def("branches")`. +* Utiliser RStudio pour créer une branche ou naviguer entre les `branches` ; +* Utiliser les interfaces `Github` ou `Gitlab` pour fusionner deux `branches`. Sur ce point, vous pouvez consulter la formation [Travail collaboratif avec R](https://linogaliana.gitlab.io/collaboratif/git.html). ::: @@ -102,7 +106,7 @@ avec vos collègues ou stocker vos codes personnels. Deux points sont importants La marche à suivre pour créer un dépôt distant est -très similaire dans `Gitlab` et dans `Github`. Les seules différences entre les deux plateformes portent sur la dénomination (un dépôt s'appelle `r with_def('repository')` sur `Github` et `project` sur `Gitlab`) et sur l'endroit où il faut cliquer pour créer un dépôt : +très similaire dans `Gitlab` et dans `Github`. Les seules différences entre les deux plateformes portent sur la dénomination (un dépôt s'appelle `repository` sur `Github` et `project` sur `Gitlab`) et sur l'endroit où il faut cliquer pour créer un dépôt : * Sur `Gitlab`, il suffit de cliquer sur `New project` dans la partie supérieure de la fenêtre : @@ -143,7 +147,7 @@ Choisir la méthode d'authentification désirée, `SSH` ou `HTTPS` #### Etape 3 : Créer un projet RStudio en clonant le dépôt distant -**La troisième étape consiste à `r with_def("cloner")` le dépôt distant** (`git clone`) c'est-à-dire à créer un projet RStudio sur votre poste local qui est une copie du dépôt distant (voir fiche XXXX pour plus de détails sur les projets RStudio). Cliquer sur `File > New Project...`, puis choisissez la troisième option (_Version Control_) : +**La troisième étape consiste à `cloner` le dépôt distant** (`git clone`) c'est-à-dire à créer un projet RStudio sur votre poste local qui est une copie du dépôt distant (voir fiche XXXX pour plus de détails sur les projets RStudio). Cliquer sur `File > New Project...`, puis choisissez la troisième option (_Version Control_) : ```{r, echo = FALSE, out.width = '65%'} utilitr::include_image("../pics/git/create_project_1.png", compression = FALSE) @@ -190,7 +194,7 @@ usethis::use_git() Cette fonction réalise deux opérations : - elle crée automatiquement tous les fichiers de configuration nécessaires au bon fonctionnement de `Git` dans le projet sur lequel vous travaillez ; -- elle effectue un premier `r with_def("commit")` (voir [cette section](#etape-2-valider-la-sauvegarde-des-modifications)) pour valider la création de ces fichiers de configuration. +- elle effectue un premier `commit` (voir [cette section](#etape-2-valider-la-sauvegarde-des-modifications)) pour valider la création de ces fichiers de configuration. La fonction `usethis::use_git()` va finalement vous proposer de sauvegarder les fichiers qui figurent déjà dans votre projet (par exemple, les codes `R` et les fichiers `csv` présents dans votre projet). Si vous avez des fichiers qui ne doivent pas être sous contrôle de version (notamment des données), il est préférable de refuser cette possibilité (en choisissant le chiffre qui correspond à "Non" parmi la liste de choix), puis de procéder comme ceci : @@ -206,10 +210,10 @@ Cette étape est identique à celle qui est décrite dans la section [Créer le La troisième étape consiste à établir un lien entre votre projet local et un dépôt distant (`git add remote`). Dans le langage `Git`, -le dépôt distant s'appelle un `r with_def("remote")`. +le dépôt distant s'appelle un `remote`. Pour créer ce lien avec l'interface de `RStudio`, il faut se rendre dans la partie destinée à -la gestion des `r with_def("branches")` sur laquelle la partie [RStudio et les branches](#git-branches) revient plus en détails. +la gestion des `branches` sur laquelle la partie [RStudio et les branches](#git-branches) revient plus en détails. ```{r, echo = FALSE, out.width = '80%'} utilitr::include_image("../pics/git/add_remote2.png", compression = FALSE) @@ -298,13 +302,13 @@ utilitr::include_image("../pics/git/create_project_3.png", compression = FALSE) C'est grâce à cette interface que vous pourrez effectuer la plupart des opérations `Git` courantes, qui sont présentées ci-dessous. Les principales commandes de cette interface sont les suivantes : -- `r with_def("Commit")` : valider les modifications d'un ou plusieurs fichier(s) ; -- `r with_def("Pull")` : récupérer sur le dépôt distant les modifications apportées au projet par d'autres contributeurs ; -- `r with_def("Push")` : partager sur le dépôt distant les modifications que vous avez apportées au projet ; +- `Commit` : valider les modifications d'un ou plusieurs fichier(s) ; +- `Pull` : récupérer sur le dépôt distant les modifications apportées au projet par d'autres contributeurs ; +- `Push` : partager sur le dépôt distant les modifications que vous avez apportées au projet ; - `History` : consulter l'historique des modifications du projet ; - `More` : ajouter des fichiers à ignorer ou revenir en arrière ou utiliser le terminal ; -- `New Branch` : créer une nouvelle `r with_def("branche")` dans le dépôt `Git` ; -- le menu déroulant tout à droite permet de changer de `r with_def("branche")`. +- `New Branch` : créer une nouvelle `branche` dans le dépôt `Git` ; +- le menu déroulant tout à droite permet de changer de `branche`. ::: {.callout-note} Si l'onglet `Git` n'apparaît pas dans la fenêtre RStudio, c'est que votre projet RStudio n'est pas encore configuré pour utiliser `Git`. Reportez-vous à la section [Initialiser l'usage de `Git` dans un projet RStudio]. @@ -374,7 +378,7 @@ utilitr::include_image("../pics/git/statut_renamed.png", compression = FALSE) La seconde étape (`git commit`) consiste à valider les modifications choisies à l'étape précédente. Pour ce faire, il faut cliquer sur le -bouton `r with_def("commit")`, situé au-dessus de la liste des +bouton commit, situé au-dessus de la liste des fichiers modifiés. En cliquant sur ce bouton, une nouvelle fenêtre s'ouvre : ```{r, echo = FALSE, out.width= '100%'} @@ -383,10 +387,10 @@ utilitr::include_image("../pics/git/onglet_git4.png", compression = FALSE) Les modifications apportées à chaque fichier sont résumées ligne à ligne dans la partie inférieure (suppressions en rouge, ajouts en vert). -Pour valider ces modifications (`r with_def("commit")`), +Pour valider ces modifications (`commit`), il faut écrire un message qui décrit la nature des modifications sauvegardées (dans le cadre vert) puis cliquer sur le -bouton `r with_def("commit")` (ovale rouge). Une fenêtre s'ouvre alors +bouton `commit` (ovale rouge). Une fenêtre s'ouvre alors et confirme que la modification a été sauvegardée : ```{r, echo = FALSE, out.width= '80%'} @@ -401,9 +405,9 @@ Il est possible, depuis `RStudio`, de consulter la liste des modifications appor utilitr::include_image("../pics/git/onglet_git6.png", compression = FALSE) ``` -Cette action ouvre une fenêtre avec la liste des `with_def("commits")` réalisée sur la -`r with_def("branches")` (voir plus bas pour la notion de `r with_def("branches")`), avec -les modifications apportées par chaque `r with_def("commit")`. Cette interface +Cette action ouvre une fenêtre avec la liste des `commits` réalisée sur la +`branches` (voir plus bas pour la notion de `branches`), avec +les modifications apportées par chaque commit. Cette interface permet de balayer rapidement les modifications apportées aux fichiers, par exemple pour retrouver à quel moment une ligne de code a été modifiée. @@ -421,12 +425,12 @@ En revanche, si vous souhaitez revenir à un état plus ancien d'un fichier, il Après avoir effectué des opérations sur son dépôt local, on peut effectuer deux opérations pour interagir avec le dépôt distant. Les boutons dans `RStudio` illustrent bien les opérations en question : -* `r with_def("pull")` +* pull ```{r, out.width="3%", out.extra='style="display: inline-block; padding: 0;"', echo = FALSE} utilitr::include_image("../pics/git/pull.png", compression = FALSE) ``` : récupérer les modifications présentes sur le dépôt distant ; -* `r with_def("push")` +* push ```{r, out.width="3%", out.extra='style="display: inline-block; padding: 0;"', echo = FALSE} utilitr::include_image("../pics/git/push.png", compression = FALSE) ``` @@ -435,7 +439,7 @@ utilitr::include_image("../pics/git/push.png", compression = FALSE) Lorsque vous partagez les modifications que vous avez apportées au projet, vos modifications viennent s'ajouter à la dernière version commune disponible (celle qui figure dans le dépôt commun). C'est pourquoi il est nécessaire que votre dépôt local soit à jour de toutes les modifications partagées par les autres contributeurs avant de partager vos modifications. **Il faut donc toujours récupérer la dernière version du projet sur le dépôt distant (en cliquant sur `pull`) avant d'envoyer des modifications (en cliquant sur `push`).** ::: {.callout-note} -Les icônes de l'onglet `Git` sont placées dans l'ordre des actions à réaliser afin de publier un code sur un dépôt distant : (add), `r `with_def("commit")`, `r with_def("pull")`, `r `with_def("push")` +Les icônes de l'onglet `Git` sont placées dans l'ordre des actions à réaliser afin de publier un code sur un dépôt distant : (add), commit, pull, push ```{r, echo = FALSE, out.width= "75%"} utilitr::include_image("../pics/git/onglet_git7.png", compression = FALSE) @@ -446,20 +450,20 @@ Il peut arriver que d'autres contributeurs aient partagé sur le dépôt distant ## RStudio et les branches {#git-branches} -### La notion de `r with_def("branche")` +### La notion de `branche` Les **branches** sont l'une des fonctionnalités les plus puissantes -de la gestion de version. La création de `r with_def("branches")` dans un projet permet +de la gestion de version. La création de `branches` dans un projet permet de développer des codes sans modifier la version de référence des codes, et donc de faire cohabiter dans un projet plusieurs versions des mêmes codes sans risque de confusion. `Git` propose également des fonctions pour fusionner facilement des versions différentes des mêmes codes. Deux points sont particulièrement importants : -- Dans un projet collaboratif, il existe une `r with_def("branche")` particulière, appelée le plus souvent `main` ou `master`, qui joue le rôle de version de référence. C’est autour d’elle que se développent les `r with_def("branches")`. -- Les modifications faites sur les codes dans une `r with_def("branche")` n'altèrent pas la version de référence (celle de la `r with_def("branche")` `master`) tant qu'il n'y a pas de fusion -entre `r with_def("branches")` (`r with_def("merge")`). +- Dans un projet collaboratif, il existe une `branche` particulière, appelée le plus souvent `main` ou `master`, qui joue le rôle de version de référence. C’est autour d’elle que se développent les `branches`. +- Les modifications faites sur les codes dans une `branche` n'altèrent pas la version de référence (celle de la `branche` `master`) tant qu'il n'y a pas de fusion +entre `branches` (`merge`). -### Créer et utiliser des `r with_def("branches")` avec RStudio +### Créer et utiliser des `branches` avec RStudio La partie droite de l'interface `git` de RStudio permet de travailler avec -des `r with_def("branches")`. +des `branches`. ```{r, echo = FALSE, out.width = "100%"} utilitr::include_image("../pics/git/onglet_git8.png", compression = FALSE) @@ -467,10 +471,10 @@ utilitr::include_image("../pics/git/onglet_git8.png", compression = FALSE) Cette interface offre principalement deux fonctions : -- **Créer une nouvelle branche** (cadre orange) : si vous cliquez sur ce bouton, une boîte de dialogue s'ouvre, dans laquelle vous devrez définir le nom de la nouvelle `r with_def("branche")` L'instruction correspondante en ligne de commande est `git checkout -b ma-branche`, où `ma-branche` est le nom de la nouvelle `r with_def("branche")` Deux points sont à noter: - - La `r with_def("branche")` source, à partir de laquelle la nouvelle `r with_def("branche")` diverge, sera celle sur laquelle vous vous situez au moment de la création. - - Il est recommandé de se placer sur `master` avant chaque création de nouvelle `r with_def("branche")`. -- **Naviguer parmi les branches** (cadre bleu) : le menu déroulant affiche d'abord la liste des branches disponibles dans votre dépôt local (`LOCAL BRANCHES`) puis la liste des branches existantes sur le dépôt distant (`REMOTE: ORIGIN`). Pour afficher le contenu d'une `r with_def("branche")`, il suffit de cliquer sur le nom de cette `r with_def("branche")`. L'instruction correspondante en ligne de commande est `git checkout ma-branche`, où `ma-branche` est le nom de la `r with_def("branche")` dont vous souhaitez afficher le contenu. +- **Créer une nouvelle branche** (cadre orange) : si vous cliquez sur ce bouton, une boîte de dialogue s'ouvre, dans laquelle vous devrez définir le nom de la nouvelle `branche` L'instruction correspondante en ligne de commande est `git checkout -b ma-branche`, où `ma-branche` est le nom de la nouvelle `branche` Deux points sont à noter: + - La `branche` source, à partir de laquelle la nouvelle `branche` diverge, sera celle sur laquelle vous vous situez au moment de la création. + - Il est recommandé de se placer sur `master` avant chaque création de nouvelle `branche`. +- **Naviguer parmi les branches** (cadre bleu) : le menu déroulant affiche d'abord la liste des branches disponibles dans votre dépôt local (`LOCAL BRANCHES`) puis la liste des branches existantes sur le dépôt distant (`REMOTE: ORIGIN`). Pour afficher le contenu d'une `branche`, il suffit de cliquer sur le nom de cette `branche`. L'instruction correspondante en ligne de commande est `git checkout ma-branche`, où `ma-branche` est le nom de la `branche` dont vous souhaitez afficher le contenu. ::: {.callout-note} L'interface graphique de RStudio ne permet pas de réaliser toutes les opérations possibles sur les branches. En particulier, il n'est pas possible de fusionner des branches avec cette interface. Les interfaces des forges (telles que `Gitlab`, `Github`...) sont beaucoup plus adaptées pour mener ce type d'opération. Vous pouvez en apprendre davantage en consultant la [formation Travail collaboratif avec `R`](https://linogaliana.gitlab.io/collaboratif/). @@ -478,9 +482,9 @@ L'interface graphique de RStudio ne permet pas de réaliser toutes les opératio ## Utiliser le terminal {#terminal-git} -Utiliser `Git` avec la ligne de commande permet de faire davantage de choses qu'avec l'interface `RStudio`. Grâce à elle, on peut par exemple corriger une maladresse, ou fusionner des `r with_def("branches")` sans utiliser l'interface d'une forge. L'utilisation de la ligne de commande est toutefois moins facile pour les débutants. +Utiliser `Git` avec la ligne de commande permet de faire davantage de choses qu'avec l'interface `RStudio`. Grâce à elle, on peut par exemple corriger une maladresse, ou fusionner des `branches` sans utiliser l'interface d'une forge. L'utilisation de la ligne de commande est toutefois moins facile pour les débutants. -L'utilisation de la ligne de commande n'est pas plus risquée que l'interface RStudio, à condition de respecter une règle simple : il ne faut __jamais exécuter une commande qui comprend les termes `force` ou `r with_def('rebase')`__. En effet, ces options peuvent créer des conflits insolubles, voire rendre le projet inutilisable par vos collaborateurs. +L'utilisation de la ligne de commande n'est pas plus risquée que l'interface RStudio, à condition de respecter une règle simple : il ne faut __jamais exécuter une commande qui comprend les termes `force` ou `rebase`__. En effet, ces options peuvent créer des conflits insolubles, voire rendre le projet inutilisable par vos collaborateurs. Pour ouvrir un terminal `Git`, cliquer sur l'écrou dans l'onglet `Git`: @@ -499,7 +503,6 @@ Vous pouvez en apprendre davantage sur l'utilisation de la ligne de commande dan ## Pour en savoir plus {#RessourcesUsageGit} -* [Formation Travail collaboratif avec `R`](https://linogaliana.gitlab.io/collaboratif/git.html) * [Travailler avec Git via RStudio et versionner son code (thinkr.fr)](https://thinkr.fr/travailler-avec-git-via-rstudio-et-versionner-son-code) * [*Happy Git with R*](https://happygitwithr.com/) * [Une présentation vidéo d'une utilisation `Git` pour débutants faite à l'Insee](https://www.youtube.com/watch?v=lyzWU43DJ9I) diff --git a/03_Fiches_thematiques/Fiche_rmarkdown.qmd b/03_Fiches_thematiques/Fiche_rmarkdown.qmd index e2ab93c9..e4daa4c0 100644 --- a/03_Fiches_thematiques/Fiche_rmarkdown.qmd +++ b/03_Fiches_thematiques/Fiche_rmarkdown.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Produire des documents avec `R Markdown` {#rmarkdown} diff --git a/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd b/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd index 89fd7745..3760efd7 100644 --- a/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd +++ b/03_Fiches_thematiques/Fiche_rmarkdown_param_report.qmd @@ -169,6 +169,10 @@ params: Il faut ensuite remplacer dans les différents _chunks_ le code du département par `params$codeDpt`. Une fois ces 2 modifications (en-tête et _chunks_) effectués, il n'est plus besoin de changer le département qu'à un seul endroit. +--- +eval: false +--- + ### Utiliser un modèle de rapport paramétré Une fois que le modèle de rapport paramétré est défini, il est possible de l'utiliser pour publier facilement des rapports. La compilation du code source avec la commande `rmarkdown::render("rapportParametre.Rmd")` générera le document suivant : diff --git a/03_Fiches_thematiques/Fiche_rprojects.qmd b/03_Fiches_thematiques/Fiche_rprojects.qmd index 9530c399..b184c288 100644 --- a/03_Fiches_thematiques/Fiche_rprojects.qmd +++ b/03_Fiches_thematiques/Fiche_rprojects.qmd @@ -1,3 +1,7 @@ +--- +eval: false +--- + # Utiliser les projets `RStudio` {#rproject} ::: {.callout-important} diff --git a/DESCRIPTION b/DESCRIPTION deleted file mode 100644 index 679624bb..00000000 --- a/DESCRIPTION +++ /dev/null @@ -1,111 +0,0 @@ -Package: documentationR -Type: Book -Title: Documentation R de l'Insee -Version: 0.8.0 -Description: Ce dépôt comprend les fichiers relatifs à la - documentation R de l'Insee. -Authors@R: c( - person("Lino" , "Galiana" , role = c("aut", "cre"), email = "lino.galiana@insee.fr"), - person("Olivier" , "Meslin" , role = c("aut", "cre"), email = "olivier.meslin@insee.fr"), - person("Gilles" , "Fidani" , role = "ctb", email = "gilles.fidani@insee.fr"), - person("Pierre" , "Lamarche" , role = "ctb", email = "pierre.lamarche@insee.fr"), - person("Gaëlle" , "Genin" , role = "ctb", email = "gaelle.genin@insee.fr"), - person("Romain" , "Lesur" , role = "ctb", email = "romain.lesur@insee.fr"), - person("Pierre-Yves" , "Berrard" , role = "ctb", email = "pierre-yves.berrard@insee.fr"), - person("Cédric" , "Tassart" , role = "ctb", email = "cedric.tassart@insee.fr"), - person("Pascal" , "Mercier" , role = "ctb", email = "pascal.mercier@insee.fr"), - person("Arthur" , "Cazaubiel" , role = "ctb", email = "arthur.cazaubiel@insee.fr"), - person("Arlindo" , "Dos Santos", role = "ctb", email = "arlindo.dos-santos@insee.fr"), - person("Alexis" , "Eidelman" , role = "ctb", email = "alexis.eidelman@travail.gouv.fr"), - person("Claire" , "Legroux" , role = "ctb", email = "claire.legroux@insee.fr"), - person("Lionel" , "Cacheux" , role = "ctb", email = "lionel.cacheux@insee.fr"), - person("Marie-Emmanuelle", "Faure" , role = "ctb", email = "marie-emmanuelle.faure@insee.fr"), - person("Mathias" , "André" , role = "ctb", email = "mathias.andre@insee.fr"), - person("Sylvain" , "Daubrée" , role = "ctb", email = "sylvain.daubree@insee.fr"), - person("Raphaële" , "Adjerad" , role = "ctb", email = "raphaele.adjerad@sante.gouv.fr"), - person("Jean-Daniel" , "Lomenède" , role = "ctb", email = "jean-daniel.lomenede@developpement-durable.gouv.fr"), - person("Géraldine" , "Rochambeau", role = "ctb", email = "geraldine.Rochambeau@justice.gouv.fr"), - person("Milena" , "Suarez Castillo", role = "ctb", email = "milena.suarez-castillo@insee.fr"), - person("Violaine" , "Poirot" , role = "ctb", email = "violaine.poirot@justice.gouv.fr"), - person("Frédérique" , "Cornuau" , role = "ctb", email = "frederique.cornuau@justice.gouv.fr"), - person("Clément" , "Rousset" , role = "ctb", email = "clement.rousset@insee.fr"), - person("Aurélien" , "D'Isanto" , role = "ctb", email = "aurelien.disanto@insee.fr"), - person("Sébastien" , "Li-Thiao-Té", role = "ctb", email = "sebastien.li-thiao-te@travail.gouv.fr"), - person(given = NULL, family = "Institut National de la Statistique et des Études Économiques", role = "cph") - ) -License: Licence Ouverte 2.0 -Encoding: UTF-8 -URL: https://github.com/InseeFrLab/utilitR -VignetteBuilder: knitr -Imports: - base, - utils, - xfun (>= 0.19), - rmarkdown, - bookdown, - pagedown (>= 0.13.11), - data.table, - readr, - openxlsx, - import, - FactoMineR, - factoextra, - corrplot, - tmap, - ggplot2, - cartography, - import, - htmltools (>= 0.5.1), - doremifasolData, - readODS, - kableExtra, - fontawesome, - magick, - magrittr, - sass, - bslib, - downlit, - utilitr, - usethis, - renv, - remotes, - targets, - lintr, - parsedate, - lubridate, - zoo, - dygraphs, - yaml, - knitr, - desc, - dplyr, - MASS, - httr, - jsonlite, - arrow, - parallel, - tools, - stringr, - sf, - units, - rex, - duckdb, - DBI, - scales, - viridis, - readxl, - tibble, - tidyr, - doremifasol, - shiny -Suggests: - cranlogs, - haven, - rprojroot -Remotes: - rstudio/htmltools@v0.5.1, - rstudio/sass, - yihui/xfun, - InseeFrLab/utilitr-template, - hadley/emo, - InseeFrLab/doremifasolData@v0.2.0 diff --git a/Dockerfile b/Dockerfile index e501a492..8b82e01c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,15 +1,12 @@ -FROM inseefrlab/onyxia-rstudio:r4.3.2-2024.02.13 +FROM inseefrlab/onyxia-rstudio:r4.4.1-2024.10.14 # R packages COPY ./DESCRIPTION /tmp/build_image/ -RUN Rscript -e "install.packages(c('xfun','knitr', 'insee', 'OECD', 'htmltools'))" -RUN Rscript -e "remotes::install_deps('/tmp/build_image', dependencies = TRUE, upgrade = FALSE)" -RUN Rscript -e "remotes::install_github('kevinushey/rex')" -RUN Rscript -e "remotes::install_github('inseefrlab/inseelocaldata')" +RUN Rscript -e "install.packages(c('renv','yaml'))" RUN apt-get update \ && apt-get -qq install gnupg - + RUN sh -c 'echo "deb http://http.us.debian.org/debian stable main contrib non-free" >> /etc/apt/sources.list' \ && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138 \ && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9 \ diff --git a/DocumentationR.Rproj b/DocumentationR.Rproj index 9eddaec0..6dbf42ab 100644 --- a/DocumentationR.Rproj +++ b/DocumentationR.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: e36da726-4a73-4cf5-bbff-99a6556f0a68 RestoreWorkspace: No SaveWorkspace: No diff --git a/README.md b/README.md index 1c9a82a7..4589ed76 100644 --- a/README.md +++ b/README.md @@ -35,6 +35,7 @@ Un environnement prêt à l'emploi est disponible pour les utilisateurs du `SSPC
+ ## :two: Objectifs de la documentation :book: ### Public cible diff --git a/_quarto.yml b/_quarto.yml index 9beef0ef..33fd4a71 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -106,7 +106,6 @@ book: - part: "Éléments de configuration" chapters: - 01_R_Insee/Fiche_utiliser_Rstudio_AUSv3.qmd - - 01_R_Insee/Fiche_utiliser_Rstudio_SSPCloud.qmd - 03_Fiches_thematiques/Fiche_configurer_git.qmd - 01_R_Insee/Fiche-personnaliser-R.qmd - 01_R_Insee/Fiche_utiliser_ressources.qmd diff --git a/docker/dependencies.sh b/docker/dependencies.sh new file mode 100755 index 00000000..6c70f511 --- /dev/null +++ b/docker/dependencies.sh @@ -0,0 +1,32 @@ +#!/bin/bash + +# Update package lists +apt-get update && apt-get -qq install gnupg + +# Install necessary packages without recommended dependencies +apt-get -qq install --no-install-recommends \ + libssl-dev + +apt-get -qq install --no-install-recommends \ + imagemagick \ + libmagick++-dev \ + ghostscript \ + libglpk40 \ + libgdal-dev libgeos-dev \ + libudunits2-dev + +apt-get -qq install --no-install-recommends \ + libgs-dev \ + librsvg2-dev \ + libwebp-dev \ + jq + +# Clean up apt cache +rm -rf /var/lib/apt/lists/* && rm -rf /src/*.deb + +# Upgrade packages +apt-get upgrade -y + +# Install mc (MinIO Client) +wget https://dl.min.io/client/mc/release/linux-amd64/mc -O /usr/local/bin/mc && \ + chmod +x /usr/local/bin/mc diff --git a/index.qmd b/index.qmd index 8dcb9f15..13270199 100644 --- a/index.qmd +++ b/index.qmd @@ -5,7 +5,7 @@ ::::: {.headline .g-col-lg-9 .g-col-12 .g-col-md-12} :::::: h1 -`utilitR` +utilitR :::::: diff --git a/renv.lock b/renv.lock new file mode 100644 index 00000000..627b2a5b --- /dev/null +++ b/renv.lock @@ -0,0 +1,8484 @@ +{ + "R": { + "Version": "4.4.2", + "Repositories": [ + { + "Name": "CRAN", + "URL": "https://packagemanager.posit.co/cran/latest" + } + ] + }, + "Packages": { + "AsioHeaders": { + "Package": "AsioHeaders", + "Version": "1.22.1-2", + "Source": "Repository", + "Type": "Package", + "Title": "'Asio' C++ Header Files", + "Date": "2022-12-07", + "Author": "Dirk Eddelbuettel", + "Maintainer": "Dirk Eddelbuettel ", + "Description": "'Asio' is a cross-platform C++ library for network and low-level I/O programming that provides developers with a consistent asynchronous model using a modern C++ approach. It is also included in Boost but requires linking when used with Boost. Standalone it can be used header-only (provided a recent compiler). 'Asio' is written and maintained by Christopher M. Kohlhoff, and released under the 'Boost Software License', Version 1.0.", + "Copyright": "file inst/COPYRIGHTS", + "License": "BSL-1.0", + "URL": "https://github.com/eddelbuettel/asioheaders, https://dirk.eddelbuettel.com/code/asioheaders.html", + "BugReports": "https://github.com/eddelbuettel/asioheaders/issues", + "NeedsCompilation": "no", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "DBI": { + "Package": "DBI", + "Version": "1.2.3", + "Source": "Repository", + "Title": "R Database Interface", + "Date": "2024-06-02", + "Authors@R": "c( person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Kirill\", \"Müller\", , \"kirill@cynkra.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1416-3412\")), person(\"R Consortium\", role = \"fnd\") )", + "Description": "A database interface definition for communication between R and relational database management systems. 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This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.", + "License": "MIT + file LICENSE", + "URL": "https://broom.tidymodels.org/, https://github.com/tidymodels/broom", + "BugReports": "https://github.com/tidymodels/broom/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "backports", + "dplyr (>= 1.0.0)", + "generics (>= 0.0.2)", + "glue", + "lifecycle", + "purrr", + "rlang", + "stringr", + "tibble (>= 3.0.0)", + "tidyr (>= 1.0.0)" + ], + "Suggests": [ + "AER", + "AUC", + "bbmle", + "betareg (>= 3.2-1)", + "biglm", + "binGroup", + "boot", + "btergm (>= 1.10.6)", + "car (>= 3.1-2)", + "carData", + "caret", + "cluster", + "cmprsk", + 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Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (), Jasper Cooper [ctb] (), E Auden Krauska [ctb] (), Alex Wang [ctb], Malcolm Barrett [ctb] (), Charles Gray [ctb] (), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (), Eduard Szoecs [ctb], Frederik Aust [ctb] (), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (), Bruna Wundervald [ctb] (), Joyce Cahoon [ctb] (), Grant McDermott [ctb] (), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (), Lukas Wallrich [ctb] (), James Martherus [ctb] (), Chuliang Xiao [ctb] (), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (), Ilaria Prosdocimi [ctb] (), Daniel D. Sjoberg [ctb] (), Alex Reinhart [ctb] ()", + "Maintainer": "Simon Couch ", + "Repository": "RSPM" + }, + "bslib": { + "Package": "bslib", + "Version": "0.8.0", + "Source": "Repository", + "Title": "Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'", + "Authors@R": "c( person(\"Carson\", \"Sievert\", , \"carson@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = \"aut\"), person(\"Garrick\", \"Aden-Buie\", , \"garrick@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(, \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Javi\", \"Aguilar\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap colorpicker library\"), person(\"Thomas\", \"Park\", role = c(\"ctb\", \"cph\"), comment = \"Bootswatch library\"), person(, \"PayPal\", role = c(\"ctb\", \"cph\"), comment = \"Bootstrap accessibility plugin\") )", + "Description": "Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. 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Much extended the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".", + "Maintainer": "Martin Maechler ", + "Authors@R": "c(person(\"Martin\",\"Maechler\", role = c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\", comment = c(ORCID = \"0000-0002-8685-9910\")) ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"peter.rousseeuw@kuleuven.be\", comment = c(\"Fortran original\", ORCID = \"0000-0002-3807-5353\")) ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\") ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment = c(\"S original\", ORCID = \"0000-0001-6398-4850\")) ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"), email=\"Kurt.Hornik@R-project.org\", comment=c(\"port to R; maintenance(1999-2000)\", ORCID=\"0000-0003-4198-9911\")) ,person(\"Matthias\", \"Studer\", role=\"ctb\") ,person(\"Pierre\", \"Roudier\", role=\"ctb\") ,person(\"Juan\", \"Gonzalez\", role=\"ctb\") ,person(\"Kamil\", \"Kozlowski\", role=\"ctb\") ,person(\"Erich\", \"Schubert\", role=\"ctb\", comment = c(\"fastpam options for pam()\", ORCID = \"0000-0001-9143-4880\")) ,person(\"Keefe\", \"Murphy\", role=\"ctb\", comment = \"volume.ellipsoid({d >= 3})\") #not yet ,person(\"Fischer-Rasmussen\", \"Kasper\", role = \"ctb\", comment = \"Gower distance for CLARA\") )", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "grDevices", + "stats", + "utils" + ], + "Suggests": [ + "MASS", + "Matrix" + ], + "SuggestsNote": "MASS: two examples using cov.rob() and mvrnorm(); Matrix tools for testing", + "Enhances": [ + "mvoutlier", + "fpc", + "ellipse", + "sfsmisc" + ], + "EnhancesNote": "xref-ed in man/*.Rd", + "LazyLoad": "yes", + "LazyData": "yes", + "ByteCompile": "yes", + "BuildResaveData": "no", + "License": "GPL (>= 2)", + "URL": "https://svn.r-project.org/R-packages/trunk/cluster/", + "NeedsCompilation": "yes", + "Author": "Martin Maechler [aut, cre] (), Peter Rousseeuw [aut] (Fortran original, ), Anja Struyf [aut] (S original), Mia Hubert [aut] (S original, ), Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000), ), Matthias Studer [ctb], Pierre Roudier [ctb], Juan Gonzalez [ctb], Kamil Kozlowski [ctb], Erich Schubert [ctb] (fastpam options for pam(), ), Keefe Murphy [ctb] (volume.ellipsoid({d >= 3}))", + "Repository": "CRAN" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Priority": "recommended", + "Author": "Luke Tierney ", + "Description": "Code analysis tools for R.", + "Title": "Code Analysis Tools for R", + "Depends": [ + "R (>= 2.1)" + ], + "Maintainer": "Luke Tierney ", + "URL": "https://gitlab.com/luke-tierney/codetools", + "License": "GPL", + "NeedsCompilation": "no", + "Repository": "CRAN" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Date": "2024-07-26", + "Title": "A Toolbox for Manipulating and Assessing Colors and Palettes", + "Authors@R": "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"), person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\", comment = c(ORCID = \"0000-0002-3224-8858\")), person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\", comment = c(ORCID = \"0000-0001-9032-8912\")), person(given = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\", comment = c(ORCID = \"0000-0002-3798-5507\")), person(given = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\")), person(given = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\", comment = c(ORCID = \"0000-0001-7346-3047\")), person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")))", + "Description": "Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. (2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ + "graphics", + "grDevices", + "stats" + ], + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "RSPM" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.2", + "Source": "Repository", + "Type": "Package", + "Title": "High Performance CommonMark and Github Markdown Rendering in R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", ,\"jeroenooms@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"John MacFarlane\", role = \"cph\", comment = \"Author of cmark\"))", + "Description": "The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including html, latex and groff man. In addition it exposes the markdown parse tree in xml format. Also includes opt-in support for GFM extensions including tables, autolinks, and strikethrough text.", + "License": "BSD_2_clause + file LICENSE", + "URL": "https://docs.ropensci.org/commonmark/ https://ropensci.r-universe.dev/commonmark", + "BugReports": "https://github.com/r-lib/commonmark/issues", + "Suggests": [ + "curl", + "testthat", + "xml2" + ], + "RoxygenNote": "7.2.3", + "Language": "en-US", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), John MacFarlane [cph] (Author of cmark)", + "Maintainer": "Jeroen Ooms ", + "Repository": "RSPM" + }, + "corrplot": { + "Package": "corrplot", + "Version": "0.95", + "Source": "Repository", + "Type": "Package", + "Title": "Visualization of a Correlation Matrix", + "Date": "2024-10-14", + "Authors@R": "c( person('Taiyun', 'Wei', email = 'weitaiyun@gmail.com', role = c('cre', 'aut')), person('Viliam', 'Simko', email = 'viliam.simko@gmail.com', role = 'aut'), person('Michael', 'Levy', email = 'michael.levy@healthcatalyst.com', role = 'ctb'), person('Yihui', 'Xie', email = 'xie@yihui.name', role = 'ctb'), person('Yan', 'Jin', email = 'jyfeather@gmail.com', role = 'ctb'), person('Jeff', 'Zemla', email = 'zemla@wisc.edu', role = 'ctb'), person('Moritz', 'Freidank', email = 'freidankm@googlemail.com', role = 'ctb'), person('Jun', 'Cai', email = 'cai-j12@mails.tsinghua.edu.cn', role = 'ctb'), person('Tomas', 'Protivinsky', email = 'tomas.protivinsky@gmail.com', role = 'ctb') )", + "Maintainer": "Taiyun Wei ", + "Suggests": [ + "seriation", + "knitr", + "RColorBrewer", + "rmarkdown", + "magrittr", + "prettydoc", + "testthat" + ], + "Description": "Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/taiyun/corrplot", + "BugReports": "https://github.com/taiyun/corrplot/issues", + "VignetteBuilder": "knitr", + "RoxygenNote": "7.2.1", + "NeedsCompilation": "no", + "Author": "Taiyun Wei [cre, aut], Viliam Simko [aut], Michael Levy [ctb], Yihui Xie [ctb], Yan Jin [ctb], Jeff Zemla [ctb], Moritz Freidank [ctb], Jun Cai [ctb], Tomas Protivinsky [ctb]", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "cowplot": { + "Package": "cowplot", + "Version": "1.1.3", + "Source": "Repository", + "Title": "Streamlined Plot Theme and Plot Annotations for 'ggplot2'", + "Authors@R": "person( given = \"Claus O.\", family = \"Wilke\", role = c(\"aut\", \"cre\"), email = \"wilke@austin.utexas.edu\", comment = c(ORCID = \"0000-0002-7470-9261\") )", + "Description": "Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization.", + "URL": "https://wilkelab.org/cowplot/", + "BugReports": "https://github.com/wilkelab/cowplot/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 3.4.0)", + "grid", + "gtable", + "grDevices", + "methods", + "rlang", + "scales" + ], + "License": "GPL-2", + "Suggests": [ + "Cairo", + "covr", + "dplyr", + "forcats", + "gridGraphics (>= 0.4-0)", + "knitr", + "lattice", + "magick", + "maps", + "PASWR", + "patchwork", + "rmarkdown", + "ragg", + "testthat (>= 1.0.0)", + "tidyr", + "vdiffr (>= 0.3.0)", + "VennDiagram" + ], + "VignetteBuilder": "knitr", + "Collate": "'add_sub.R' 'align_plots.R' 'as_grob.R' 'as_gtable.R' 'axis_canvas.R' 'cowplot.R' 'draw.R' 'get_plot_component.R' 'get_axes.R' 'get_titles.R' 'get_legend.R' 'get_panel.R' 'gtable.R' 'key_glyph.R' 'plot_grid.R' 'save.R' 'set_null_device.R' 'setup.R' 'stamp.R' 'themes.R' 'utils_ggplot2.R'", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Claus O. Wilke [aut, cre] ()", + "Maintainer": "Claus O. Wilke ", + "Repository": "RSPM" + }, + "cpp11": { + "Package": "cpp11", + "Version": "0.5.0", + "Source": "Repository", + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "RSPM" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ + "grDevices", + "methods", + "utils" + ], + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "credentials": { + "Package": "credentials", + "Version": "2.0.2", + "Source": "Repository", + "Type": "Package", + "Title": "Tools for Managing SSH and Git Credentials", + "Authors@R": "person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\"))", + "Description": "Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.", + "License": "MIT + file LICENSE", + "SystemRequirements": "git (optional)", + "Encoding": "UTF-8", + "Imports": [ + "openssl (>= 1.3)", + "sys (>= 2.1)", + "curl", + "jsonlite", + "askpass" + ], + "Suggests": [ + "testthat", + "knitr", + "rmarkdown" + ], + "RoxygenNote": "7.2.1", + "VignetteBuilder": "knitr", + "Language": "en-US", + "URL": "https://docs.ropensci.org/credentials/ https://r-lib.r-universe.dev/credentials", + "BugReports": "https://github.com/r-lib/credentials/issues", + "NeedsCompilation": "no", + "Author": "Jeroen Ooms [aut, cre] ()", + "Maintainer": "Jeroen Ooms ", + "Repository": "RSPM" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.", + "License": "MIT + file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", + "jsonlite", + "lazyeval", + "R6" + ], + "Suggests": [ + "shiny", + "ggplot2", + "testthat (>= 2.1.0)", + "sass", + "bslib" + ], + "URL": "https://rstudio.github.io/crosstalk/, https://github.com/rstudio/crosstalk", + "BugReports": "https://github.com/rstudio/crosstalk/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library)", + "Maintainer": "Carson Sievert ", + "Repository": "RSPM" + }, + "curl": { + "Package": "curl", + "Version": "5.2.3", + "Source": "Repository", + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = \"ctb\"), person(\"RStudio\", role = \"cph\") )", + "Description": "The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https, ftps), gzip compression, authentication, and other 'libcurl' goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. 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[ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "RSPM" + }, + "dbplyr": { + "Package": "dbplyr", + "Version": "2.5.0", + "Source": "Repository", + "Type": "Package", + "Title": "A 'dplyr' Back End for Databases", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Maximilian\", \"Girlich\", role = \"aut\"), person(\"Edgar\", \"Ruiz\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. 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Maximilian Girlich [aut], Edgar Ruiz [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, + "dendextend": { + "Package": "dendextend", + "Version": "1.18.1", + "Source": "Repository", + "Type": "Package", + "Title": "Extending 'dendrogram' Functionality in R", + "Date": "2024-10-12", + "Authors@R": "c(person(\"Tal\", \"Galili\", role = c(\"aut\", \"cre\", \"cph\"), email = \"tal.galili@gmail.com\", comment = \"https://www.r-statistics.com\"), person(\"Yoav\", \"Benjamini\", email = \"ybenja@tau.ac.il\",role = \"ths\"), person(\"Gavin\", \"Simpson\", role = \"ctb\"), person(\"Gregory\",\"Jefferis\", role = c(\"aut\", \"ctb\"), email = \"jefferis@gmail.com\", comment =\"imported code from his dendroextras package\"), person(\"Marco\", \"Gallotta\", role = \"ctb\", comment = \"a.k.a: marcog\") , person(\"Johan\", \"Renaudie\", role = \"ctb\", comment = \"https://github.com/plannapus\"), person(\"The R Core Team\", role = \"ctb\", comment = \"Thanks for the Infastructure, and code in the examples\"), person(\"Kurt\", \"Hornik\", role = \"ctb\"), person(\"Uwe\", \"Ligges\", role = \"ctb\"), person(\"Andrej-Nikolai\", \"Spiess\", role = \"ctb\"), person(\"Steve\", \"Horvath\",email = \"SHorvath@mednet.ucla.edu\", role = \"ctb\"), person(\"Peter\", \"Langfelder\",email = \"Peter.Langfelder@gmail.com\", role = \"ctb\"), person(\"skullkey\", role = \"ctb\"), person(\"Mark\", \"Van Der Loo\", email = \"mark.vanderloo@gmail.com\", comment = \"https://github.com/markvanderloo d3dendrogram\", role = \"ctb\"), person(\"Andrie\", \"de Vries\", email = \"apdevries@gmail.com\", comment = \"ggdendro author\", role = \"ctb\"), person(\"Zuguang\", \"Gu\", email = \"z.gu@dkfz-heidelberg.de\", comment = \"circlize author\", role = \"ctb\"), person(\"Cath\", comment = \"https://github.com/CathG\", role = \"ctb\"), person(\"John\", \"Ma\", comment = \"https://github.com/JohnMCMa\", role = \"ctb\"), person(\"Krzysiek\", \"G\", comment = 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You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. 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Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "utils" + ], + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "RSPM" + }, + "doBy": { + "Package": "doBy", + "Version": "4.6.24", + "Source": "Repository", + "Title": "Groupwise Statistics, LSmeans, Linear Estimates, Utilities", + "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", + "Maintainer": "Søren Højsgaard ", + "Description": "Utility package containing: 1) Facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear estimates. 3) Restrict functions to a smaller domain. 4) Miscellaneous other utilities.", + "Encoding": "UTF-8", + "VignetteBuilder": "knitr", + "LazyData": "true", + "LazyDataCompression": "xz", + "URL": "https://github.com/hojsgaard/doBy", + "License": "GPL (>= 2)", + "Depends": [ + "R (>= 4.2.0)", + "methods" + ], + "Imports": [ + "boot", + "broom", + "cowplot", + "Deriv", + "dplyr", + "ggplot2", + "MASS", + "Matrix", + "modelr", + "microbenchmark", + "rlang", + "tibble", + "tidyr" + ], + "Suggests": [ + "geepack", + "knitr", + "lme4", + "markdown", + "multcomp", + "pbkrtest (>= 0.5.2)", + "survival", + "testthat (>= 2.1.0)" + ], + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Ulrich Halekoh [aut, cph], Søren Højsgaard [aut, cre, cph]", + "Repository": "RSPM" + }, + "doremifasolData": { + "Package": "doremifasolData", + "Version": "0.2.0", + "Source": "GitHub", + "Title": "Companion to DoReMIFaSol Data Sets", + "Authors@R": "c( person(\"Pierre\", \"Lamarche\", email = \"pierre.lamarche@insee.fr\", role = c(\"aut\", \"cre\")), person(\"Pierre-Yves\", \"Berrard\", role = \"aut\", email = \"pierre-yves.berrard@insee.fr\"), person(family = \"Institut National de la Statistique et des Études Économiques\", role = \"cph\") )", + "Description": "Datasets from Insee's Website.", + "Language": "fr", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "doremifasol", + "knitr" + ], + "License": "MIT + file LICENSE", + "LazyData": "true", + "RoxygenNote": "7.1.1", + "Roxygen": "list(markdown = TRUE)", + "Encoding": "UTF-8", + "URL": "https://InseeFrLab.github.io/DoReMIFaSolData, https://github.com/InseeFrLab/DoReMIFaSolData", + "BugReports": "https://github.com/InseeFrLab/DoReMIFaSolData/issues", + "Author": "Pierre Lamarche [aut, cre], Pierre-Yves Berrard [aut], Institut National de la Statistique et des Études Économiques [cph]", + "Maintainer": "Pierre Lamarche ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "InseeFrLab", + "RemoteRepo": "doremifasolData", + "RemoteRef": "v0.2.0", + "RemoteSha": "7be601473a81f76aab5c3deb2f1e586f9604489e", + "Remotes": "InseeFrLab/doremifasol" + }, + "downlit": { + "Package": "downlit", + "Version": "0.4.4", + "Source": "Repository", + "Title": "Syntax Highlighting and Automatic Linking", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and 'bookdown'. 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This package includes all of DuckDB and an R Database Interface (DBI) connector.", + "License": "MIT + file LICENSE", + "URL": "https://r.duckdb.org/, https://github.com/duckdb/duckdb-r", + "BugReports": "https://github.com/duckdb/duckdb-r/issues", + "Depends": [ + "DBI", + "R (>= 3.6.0)" + ], + "Imports": [ + "methods", + "utils" + ], + "Suggests": [ + "adbcdrivermanager", + "arrow (>= 13.0.0)", + "bit64", + "callr", + "clock", + "DBItest", + "dbplyr", + "dplyr", + "rlang", + "testthat", + "tibble", + "vctrs", + "withr" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2.9000", + "Config/build/compilation-database": "true", + "NeedsCompilation": "yes", + "Author": "Hannes Mühleisen [aut] (), Mark Raasveldt [aut] (), Kirill Müller [cre] (), Stichting DuckDB Foundation [cph], Apache Software Foundation [cph], PostgreSQL Global Development Group [cph], The Regents of the University of California [cph], Cameron Desrochers [cph], Victor Zverovich [cph], RAD Game Tools [cph], Valve Software [cph], Rich Geldreich [cph], Tenacious Software LLC [cph], The RE2 Authors [cph], Google Inc. 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'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.", + "License": "GPL (>= 2)", + "LazyData": "TRUE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 3.1.0)", + "ggplot2 (>= 3.4.0)" + ], + "Imports": [ + "ggrepel (>= 0.9.2)", + "grid", + "ggsci", + "stats", + "utils", + "tidyr (>= 1.3.0)", + "purrr", + "dplyr (>= 0.7.1)", + "cowplot (>= 1.1.1)", + "ggsignif", + "scales", + "gridExtra", + "glue", + "polynom", + "rlang (>= 0.4.6)", + "rstatix (>= 0.7.2)", + "tibble", + "magrittr" + ], + "Suggests": [ + "grDevices", + "knitr", + "RColorBrewer", + "gtable", + "testthat" + ], + "URL": "https://rpkgs.datanovia.com/ggpubr/", + "BugReports": "https://github.com/kassambara/ggpubr/issues", + "RoxygenNote": "7.2.3", + "Collate": "'utilities_color.R' 'utilities_base.R' 'desc_statby.R' 'utilities.R' 'add_summary.R' 'annotate_figure.R' 'as_ggplot.R' 'as_npc.R' 'axis_scale.R' 'background_image.R' 'bgcolor.R' 'border.R' 'compare_means.R' 'create_aes.R' 'diff_express.R' 'facet.R' 'font.R' 'gene_citation.R' 'gene_expression.R' 'geom_bracket.R' 'geom_exec.R' 'utils-aes.R' 'utils_stat_test_label.R' 'geom_pwc.R' 'get_breaks.R' 'get_coord.R' 'get_legend.R' 'get_palette.R' 'ggadd.R' 'ggadjust_pvalue.R' 'ggarrange.R' 'ggballoonplot.R' 'ggpar.R' 'ggbarplot.R' 'ggboxplot.R' 'ggdensity.R' 'ggpie.R' 'ggdonutchart.R' 'stat_conf_ellipse.R' 'stat_chull.R' 'ggdotchart.R' 'ggdotplot.R' 'ggecdf.R' 'ggerrorplot.R' 'ggexport.R' 'gghistogram.R' 'ggline.R' 'ggmaplot.R' 'ggpaired.R' 'ggparagraph.R' 'ggpubr-package.R' 'ggpubr_args.R' 'ggpubr_options.R' 'ggqqplot.R' 'utilities_label.R' 'stat_cor.R' 'stat_stars.R' 'ggscatter.R' 'ggscatterhist.R' 'ggstripchart.R' 'ggsummarystats.R' 'ggtext.R' 'ggtexttable.R' 'ggviolin.R' 'gradient_color.R' 'grids.R' 'npc_to_data_coord.R' 'reexports.R' 'rotate.R' 'rotate_axis_text.R' 'rremove.R' 'set_palette.R' 'show_line_types.R' 'show_point_shapes.R' 'stat_anova_test.R' 'stat_central_tendency.R' 'stat_compare_means.R' 'stat_friedman_test.R' 'stat_kruskal_test.R' 'stat_mean.R' 'stat_overlay_normal_density.R' 'stat_pvalue_manual.R' 'stat_regline_equation.R' 'stat_welch_anova_test.R' 'text_grob.R' 'theme_pubr.R' 'theme_transparent.R' 'utils-geom-signif.R' 'utils-pipe.R' 'utils-tidyr.R'", + "NeedsCompilation": "no", + "Author": "Alboukadel Kassambara [aut, cre]", + "Maintainer": "Alboukadel Kassambara ", + "Repository": "RSPM" + }, + "ggrepel": { + "Package": "ggrepel", + "Version": "0.9.6", + "Source": "Repository", + "Authors@R": "c( person(\"Kamil\", \"Slowikowski\", email = \"kslowikowski@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2843-6370\")), person(\"Alicia\", \"Schep\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3915-0618\")), person(\"Sean\", \"Hughes\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9409-9405\")), person(\"Trung Kien\", \"Dang\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7562-6495\")), person(\"Saulius\", \"Lukauskas\", role = \"ctb\"), person(\"Jean-Olivier\", \"Irisson\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4920-3880\")), person(\"Zhian N\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(\"Thompson\", \"Ryan\", role = \"ctb\", comment = c(ORCID = \"0000-0002-0450-8181\")), person(\"Dervieux\", \"Christophe\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Yutani\", \"Hiroaki\", role = \"ctb\"), person(\"Pierre\", \"Gramme\", role = \"ctb\"), person(\"Amir Masoud\", \"Abdol\", role = \"ctb\"), person(\"Malcolm\", \"Barrett\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(\"Robrecht\", \"Cannoodt\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3641-729X\")), person(\"Michał\", \"Krassowski\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9638-7785\")), person(\"Michael\", \"Chirico\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Pedro\", \"Aphalo\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3385-972X\")), person(\"Francis\", \"Barton\", role = \"ctb\") )", + "Title": "Automatically Position Non-Overlapping Text Labels with 'ggplot2'", + "Description": "Provides text and label geoms for 'ggplot2' that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.", + "Depends": [ + "R (>= 3.0.0)", + "ggplot2 (>= 2.2.0)" + ], + "Imports": [ + "grid", + "Rcpp", + "rlang (>= 0.3.0)", + "scales (>= 0.5.0)", + "withr (>= 2.5.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "testthat", + "svglite", + "vdiffr", + "gridExtra", + "ggpp", + "patchwork", + "devtools", + "prettydoc", + "ggbeeswarm", + "dplyr", + "magrittr", + "readr", + "stringr" + ], + "VignetteBuilder": "knitr", + "License": "GPL-3 | file LICENSE", + "URL": "https://ggrepel.slowkow.com/, https://github.com/slowkow/ggrepel", + "BugReports": "https://github.com/slowkow/ggrepel/issues", + "RoxygenNote": "7.3.1", + "LinkingTo": [ + "Rcpp" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Kamil Slowikowski [aut, cre] (), Alicia Schep [ctb] (), Sean Hughes [ctb] (), Trung Kien Dang [ctb] (), Saulius Lukauskas [ctb], Jean-Olivier Irisson [ctb] (), Zhian N Kamvar [ctb] (), Thompson Ryan [ctb] (), Dervieux Christophe [ctb] (), Yutani Hiroaki [ctb], Pierre Gramme [ctb], Amir Masoud Abdol [ctb], Malcolm Barrett [ctb] (), Robrecht Cannoodt [ctb] (), Michał Krassowski [ctb] (), Michael Chirico [ctb] (), Pedro Aphalo [ctb] (), Francis Barton [ctb]", + "Maintainer": "Kamil Slowikowski ", + "Repository": "RSPM" + }, + "ggsci": { + "Package": "ggsci", + "Version": "3.2.0", + "Source": "Repository", + "Type": "Package", + "Title": "Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'", + "Authors@R": "c( person(\"Nan\", \"Xiao\", email = \"me@nanx.me\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0250-5673\")), person(\"Joshua\", \"Cook\", email = \"joshuacook0023@gmail.com\", role = \"ctb\"), person(\"Clara\", \"Jégousse\", email = \"cat3@hi.is\", role = \"ctb\"), person(\"Hui\", \"Chen\", email = \"huichen@zju.edu.cn\", role = \"ctb\"), person(\"Miaozhu\", \"Li\", email = \"miaozhu.li@duke.edu\", role = \"ctb\") )", + "Maintainer": "Nan Xiao ", + "Description": "A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.", + "License": "GPL (>= 3)", + "URL": "https://nanx.me/ggsci/, https://github.com/nanxstats/ggsci", + "BugReports": "https://github.com/nanxstats/ggsci/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "ggplot2 (>= 2.0.0)", + "grDevices", + "scales" + ], + "Suggests": [ + "gridExtra", + "knitr", + "ragg", + "rmarkdown" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Nan Xiao [aut, cre] (), Joshua Cook [ctb], Clara Jégousse [ctb], Hui Chen [ctb], Miaozhu Li [ctb]", + "Repository": "RSPM" + }, + "ggsignif": { + "Package": "ggsignif", + "Version": "0.6.4", + "Source": "Repository", + "Type": "Package", + "Title": "Significance Brackets for 'ggplot2'", + "Authors@R": "c( person(given = \"Constantin\", family = \"Ahlmann-Eltze\", role = c(\"aut\", \"cre\", \"ctb\"), email = \"artjom31415@googlemail.com\", comment = c(ORCID = \"0000-0002-3762-068X\", Twitter = \"@const_ae\")), person(given = \"Indrajeet\", family = \"Patil\", role = c(\"aut\", \"ctb\"), email = \"patilindrajeet.science@gmail.com\", comment = c(ORCID = \"0000-0003-1995-6531\", Twitter = \"@patilindrajeets\")) )", + "Description": "Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance (NS, *, **, ***). The package provides a single layer (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() etc.) as arguments and adds the annotation to the plot.", + "License": "GPL-3 | file LICENSE", + "URL": "https://const-ae.github.io/ggsignif/, https://github.com/const-ae/ggsignif", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "Imports": [ + "ggplot2 (>= 3.3.5)" + ], + "Suggests": [ + "knitr", + "rmarkdown", + "testthat", + "vdiffr (>= 1.0.2)" + ], + "RoxygenNote": "7.2.1", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "NeedsCompilation": "no", + "Author": "Constantin Ahlmann-Eltze [aut, cre, ctb] (, @const_ae), Indrajeet Patil [aut, ctb] (, @patilindrajeets)", + "Maintainer": "Constantin Ahlmann-Eltze ", + "Repository": "RSPM" + }, + "gh": { + "Package": "gh", + "Version": "1.4.1", + "Source": "Repository", + "Title": "'GitHub' 'API'", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"cre\", \"ctb\")), person(\"Jennifer\", \"Bryan\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Minimal client to access the 'GitHub' 'API'.", + "License": "MIT + file LICENSE", + "URL": "https://gh.r-lib.org/, https://github.com/r-lib/gh#readme", + "BugReports": "https://github.com/r-lib/gh/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.0.1)", + "gitcreds", + "glue", + "httr2", + "ini", + "jsonlite", + "lifecycle", + "rlang (>= 1.0.0)" + ], + "Suggests": [ + "covr", + "knitr", + "mockery", + "rmarkdown", + "rprojroot", + "spelling", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.1.9000", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [cre, ctb], Jennifer Bryan [aut], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "gitcreds": { + "Package": "gitcreds", + "Version": "0.1.2", + "Source": "Repository", + "Title": "Query 'git' Credentials from 'R'", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"RStudio\", role = c(\"cph\", \"fnd\")) )", + "Description": "Query, set, delete credentials from the 'git' credential store. Manage 'GitHub' tokens and other 'git' credentials. This package is to be used by other packages that need to authenticate to 'GitHub' and/or other 'git' repositories.", + "License": "MIT + file LICENSE", + "URL": "https://gitcreds.r-lib.org/, https://github.com/r-lib/gitcreds", + "BugReports": "https://github.com/r-lib/gitcreds/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Suggests": [ + "codetools", + "covr", + "knitr", + "mockery", + "oskeyring", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.1.9000", + "SystemRequirements": "git", + "Config/testthat/edition": "3", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], RStudio [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "glue": { + "Package": "glue", + "Version": "1.8.0", + "Source": "Repository", + "Title": "Interpreted String Literals", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "An implementation of interpreted string literals, inspired by Python's Literal String Interpolation and Docstrings and Julia's Triple-Quoted String Literals .", + "License": "MIT + file LICENSE", + "URL": "https://glue.tidyverse.org/, https://github.com/tidyverse/glue", + "BugReports": "https://github.com/tidyverse/glue/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "crayon", + "DBI (>= 1.2.0)", + "dplyr", + "knitr", + "magrittr", + "rlang", + "rmarkdown", + "RSQLite", + "testthat (>= 3.2.0)", + "vctrs (>= 0.3.0)", + "waldo (>= 0.5.3)", + "withr" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "Config/Needs/website": "bench, forcats, ggbeeswarm, ggplot2, R.utils, rprintf, tidyr, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Jennifer Bryan [aut, cre] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "RSPM" + }, + "gridExtra": { + "Package": "gridExtra", + "Version": "2.3", + "Source": "Repository", + "Authors@R": "c(person(\"Baptiste\", \"Auguie\", email = \"baptiste.auguie@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Anton\", \"Antonov\", email = \"tonytonov@gmail.com\", role = c(\"ctb\")))", + "License": "GPL (>= 2)", + "Title": "Miscellaneous Functions for \"Grid\" Graphics", + "Type": "Package", + "Description": "Provides a number of user-level functions to work with \"grid\" graphics, notably to arrange multiple grid-based plots on a page, and draw tables.", + "VignetteBuilder": "knitr", + "Imports": [ + "gtable", + "grid", + "grDevices", + "graphics", + "utils" + ], + "Suggests": [ + "ggplot2", + "egg", + "lattice", + "knitr", + "testthat" + ], + "RoxygenNote": "6.0.1", + "NeedsCompilation": "no", + "Author": "Baptiste Auguie [aut, cre], Anton Antonov [ctb]", + "Maintainer": "Baptiste Auguie ", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "gtable": { + "Package": "gtable", + "Version": "0.3.5", + "Source": "Repository", + "Title": "Arrange 'Grobs' in Tables", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Tools to make it easier to work with \"tables\" of 'grobs'. The 'gtable' package defines a 'gtable' grob class that specifies a grid along with a list of grobs and their placement in the grid. Further the package makes it easy to manipulate and combine 'gtable' objects so that complex compositions can be built up sequentially.", + "License": "MIT + file LICENSE", + "URL": "https://gtable.r-lib.org, https://github.com/r-lib/gtable", + "BugReports": "https://github.com/r-lib/gtable/issues", + "Depends": [ + "R (>= 3.5)" + ], + "Imports": [ + "cli", + "glue", + "grid", + "lifecycle", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "profvis", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "RSPM" + }, + "highr": { + "Package": "highr", + "Version": "0.11", + "Source": "Repository", + "Type": "Package", + "Title": "Syntax Highlighting for R Source Code", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Yixuan\", \"Qiu\", role = \"aut\"), person(\"Christopher\", \"Gandrud\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\") )", + "Description": "Provides syntax highlighting for R source code. 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Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.", + "License": "MIT + file LICENSE", + "URL": "http://haozhu233.github.io/kableExtra/, https://github.com/haozhu233/kableExtra", + "BugReports": "https://github.com/haozhu233/kableExtra/issues", + "Depends": [ + "R (>= 3.1.0)" + ], + "Imports": [ + "knitr (>= 1.33)", + "magrittr", + "stringr (>= 1.0)", + "xml2 (>= 1.1.1)", + "rmarkdown (>= 1.6.0)", + "scales", + "viridisLite", + "stats", + "grDevices", + "htmltools", + "rstudioapi", + "tools", + "digest", + "graphics", + "svglite" + ], + "Suggests": [ + "testthat", + "magick", + "tinytex", + "formattable", + "sparkline", + "webshot2" + ], + "Config/testthat/edition": "3", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Language": "en-US", + "NeedsCompilation": "no", + "Author": "Hao Zhu [aut, cre] (), Thomas Travison [ctb], Timothy Tsai [ctb], Will Beasley [ctb], Yihui Xie [ctb], GuangChuang Yu [ctb], Stéphane Laurent [ctb], Rob Shepherd [ctb], Yoni Sidi [ctb], Brian Salzer [ctb], George Gui [ctb], Yeliang Fan [ctb], Duncan Murdoch [ctb], Vincent Arel-Bundock [ctb], Bill Evans [ctb]", + "Maintainer": "Hao Zhu ", + "Repository": "RSPM" + }, + "knitr": { + "Package": "knitr", + "Version": "1.48", + "Source": "Repository", + "Type": "Package", + "Title": "A General-Purpose Package for Dynamic Report Generation in R", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Abhraneel\", \"Sarma\", role = \"ctb\"), person(\"Adam\", \"Vogt\", role = \"ctb\"), person(\"Alastair\", \"Andrew\", role = \"ctb\"), person(\"Alex\", \"Zvoleff\", role = \"ctb\"), person(\"Amar\", \"Al-Zubaidi\", role = \"ctb\"), person(\"Andre\", \"Simon\", role = \"ctb\", comment = \"the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de\"), person(\"Aron\", \"Atkins\", role = \"ctb\"), person(\"Aaron\", \"Wolen\", role = \"ctb\"), person(\"Ashley\", \"Manton\", role = \"ctb\"), person(\"Atsushi\", \"Yasumoto\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8335-495X\")), person(\"Ben\", \"Baumer\", role = \"ctb\"), person(\"Brian\", \"Diggs\", role = \"ctb\"), person(\"Brian\", \"Zhang\", role = \"ctb\"), person(\"Bulat\", \"Yapparov\", role = \"ctb\"), person(\"Cassio\", \"Pereira\", role = \"ctb\"), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person(\"David\", \"Hall\", role = \"ctb\"), person(\"David\", \"Hugh-Jones\", role = \"ctb\"), person(\"David\", \"Robinson\", role = \"ctb\"), person(\"Doug\", \"Hemken\", role = \"ctb\"), person(\"Duncan\", \"Murdoch\", role = \"ctb\"), person(\"Elio\", \"Campitelli\", role = \"ctb\"), person(\"Ellis\", \"Hughes\", role = \"ctb\"), person(\"Emily\", \"Riederer\", role = \"ctb\"), person(\"Fabian\", \"Hirschmann\", role = \"ctb\"), person(\"Fitch\", \"Simeon\", role = \"ctb\"), person(\"Forest\", \"Fang\", role = \"ctb\"), person(c(\"Frank\", \"E\", \"Harrell\", \"Jr\"), role = \"ctb\", comment = \"the Sweavel package at inst/misc/Sweavel.sty\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\"), person(\"Gregoire\", \"Detrez\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Hao\", \"Zhu\", role = \"ctb\"), person(\"Heewon\", \"Jeon\", role = \"ctb\"), person(\"Henrik\", \"Bengtsson\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Ian\", \"Lyttle\", role = \"ctb\"), person(\"Hodges\", \"Daniel\", role = \"ctb\"), person(\"Jacob\", \"Bien\", role = \"ctb\"), person(\"Jake\", \"Burkhead\", role = \"ctb\"), person(\"James\", \"Manton\", role = \"ctb\"), person(\"Jared\", \"Lander\", role = \"ctb\"), person(\"Jason\", \"Punyon\", role = \"ctb\"), person(\"Javier\", \"Luraschi\", role = \"ctb\"), person(\"Jeff\", \"Arnold\", role = \"ctb\"), person(\"Jenny\", \"Bryan\", role = \"ctb\"), person(\"Jeremy\", \"Ashkenas\", role = c(\"ctb\", \"cph\"), comment = \"the CSS file at inst/misc/docco-classic.css\"), person(\"Jeremy\", \"Stephens\", role = \"ctb\"), person(\"Jim\", \"Hester\", role = \"ctb\"), person(\"Joe\", \"Cheng\", role = \"ctb\"), person(\"Johannes\", \"Ranke\", role = \"ctb\"), person(\"John\", \"Honaker\", role = \"ctb\"), person(\"John\", \"Muschelli\", role = \"ctb\"), person(\"Jonathan\", \"Keane\", role = \"ctb\"), person(\"JJ\", \"Allaire\", role = \"ctb\"), person(\"Johan\", \"Toloe\", role = \"ctb\"), person(\"Jonathan\", \"Sidi\", role = \"ctb\"), person(\"Joseph\", \"Larmarange\", role = \"ctb\"), person(\"Julien\", \"Barnier\", role = \"ctb\"), person(\"Kaiyin\", \"Zhong\", role = \"ctb\"), person(\"Kamil\", \"Slowikowski\", role = \"ctb\"), person(\"Karl\", \"Forner\", role = \"ctb\"), person(c(\"Kevin\", \"K.\"), \"Smith\", role = \"ctb\"), person(\"Kirill\", \"Mueller\", role = \"ctb\"), person(\"Kohske\", \"Takahashi\", role = \"ctb\"), person(\"Lorenz\", \"Walthert\", role = \"ctb\"), person(\"Lucas\", \"Gallindo\", role = \"ctb\"), person(\"Marius\", \"Hofert\", role = \"ctb\"), person(\"Martin\", \"Modrák\", role = \"ctb\"), person(\"Michael\", \"Chirico\", role = \"ctb\"), person(\"Michael\", \"Friendly\", role = \"ctb\"), person(\"Michal\", \"Bojanowski\", role = \"ctb\"), person(\"Michel\", \"Kuhlmann\", role = \"ctb\"), person(\"Miller\", \"Patrick\", role = \"ctb\"), person(\"Nacho\", \"Caballero\", role = \"ctb\"), person(\"Nick\", \"Salkowski\", role = \"ctb\"), person(\"Niels Richard\", \"Hansen\", role = \"ctb\"), person(\"Noam\", \"Ross\", role = \"ctb\"), person(\"Obada\", \"Mahdi\", role = \"ctb\"), person(\"Pavel N.\", \"Krivitsky\", role = \"ctb\", comment=c(ORCID = \"0000-0002-9101-3362\")), person(\"Pedro\", \"Faria\", role = \"ctb\"), person(\"Qiang\", \"Li\", role = \"ctb\"), person(\"Ramnath\", \"Vaidyanathan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Robert\", \"Krzyzanowski\", role = \"ctb\"), person(\"Rodrigo\", \"Copetti\", role = \"ctb\"), person(\"Romain\", \"Francois\", role = \"ctb\"), person(\"Ruaridh\", \"Williamson\", role = \"ctb\"), person(\"Sagiru\", \"Mati\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1413-3974\")), person(\"Scott\", \"Kostyshak\", role = \"ctb\"), person(\"Sebastian\", \"Meyer\", role = \"ctb\"), person(\"Sietse\", \"Brouwer\", role = \"ctb\"), person(c(\"Simon\", \"de\"), \"Bernard\", role = \"ctb\"), person(\"Sylvain\", \"Rousseau\", role = \"ctb\"), person(\"Taiyun\", \"Wei\", role = \"ctb\"), person(\"Thibaut\", \"Assus\", role = \"ctb\"), person(\"Thibaut\", \"Lamadon\", role = \"ctb\"), person(\"Thomas\", \"Leeper\", role = \"ctb\"), person(\"Tim\", \"Mastny\", role = \"ctb\"), person(\"Tom\", \"Torsney-Weir\", role = \"ctb\"), person(\"Trevor\", \"Davis\", role = \"ctb\"), person(\"Viktoras\", \"Veitas\", role = \"ctb\"), person(\"Weicheng\", \"Zhu\", role = \"ctb\"), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Zachary\", \"Foster\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1458-7108\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "evaluate (>= 0.15)", + "highr (>= 0.11)", + "methods", + "tools", + "xfun (>= 0.44)", + "yaml (>= 2.1.19)" + ], + "Suggests": [ + "bslib", + "codetools", + "DBI (>= 0.4-1)", + "digest", + "formatR", + "gifski", + "gridSVG", + "htmlwidgets (>= 0.7)", + "jpeg", + "JuliaCall (>= 0.11.1)", + "magick", + "markdown (>= 1.3)", + "png", + "ragg", + "reticulate (>= 1.4)", + "rgl (>= 0.95.1201)", + "rlang", + "rmarkdown", + "sass", + "showtext", + "styler (>= 1.2.0)", + "targets (>= 0.6.0)", + "testit", + "tibble", + "tikzDevice (>= 0.10)", + "tinytex (>= 0.46)", + "webshot", + "rstudioapi", + "svglite" + ], + "License": "GPL", + "URL": "https://yihui.org/knitr/", + "BugReports": "https://github.com/yihui/knitr/issues", + "Encoding": "UTF-8", + "VignetteBuilder": "knitr", + "SystemRequirements": "Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", + "Collate": "'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" + }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Type": "Package", + "Title": "Axis Labeling", + "Date": "2023-08-29", + "Author": "Justin Talbot,", + "Maintainer": "Nuno Sempere ", + "Description": "Functions which provide a range of axis labeling algorithms.", + "License": "MIT + file LICENSE | Unlimited", + "Collate": "'labeling.R'", + "NeedsCompilation": "no", + "Imports": [ + "stats", + "graphics" + ], + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "later": { + "Package": "later", + "Version": "1.3.2", + "Source": "Repository", + "Type": "Package", + "Title": "Utilities for Scheduling Functions to Execute Later with Event Loops", + "Authors@R": "c( person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@posit.co\"), person(\"Joe\", \"Cheng\", role = c(\"aut\"), email = \"joe@posit.co\"), person(family = \"Posit Software, PBC\", role = \"cph\"), person(\"Marcus\", \"Geelnard\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\"), person(\"Evan\", \"Nemerson\", role = c(\"ctb\", \"cph\"), comment = \"TinyCThread library, https://tinycthread.github.io/\") )", + "Description": "Executes arbitrary R or C functions some time after the current time, after the R execution stack has emptied. The functions are scheduled in an event loop.", + "URL": "https://r-lib.github.io/later/, https://github.com/r-lib/later", + "BugReports": "https://github.com/r-lib/later/issues", + "License": "MIT + file LICENSE", + "Imports": [ + "Rcpp (>= 0.12.9)", + "rlang" + ], + "LinkingTo": [ + "Rcpp" + ], + "RoxygenNote": "7.2.3", + "Suggests": [ + "knitr", + "rmarkdown", + "testthat (>= 2.1.0)" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Winston Chang [aut, cre], Joe Cheng [aut], Posit Software, PBC [cph], Marcus Geelnard [ctb, cph] (TinyCThread library, https://tinycthread.github.io/), Evan Nemerson [ctb, cph] (TinyCThread library, https://tinycthread.github.io/)", + "Maintainer": "Winston Chang ", + "Repository": "RSPM" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository", + "Date": "2024-03-20", + "Priority": "recommended", + "Title": "Trellis Graphics for R", + "Authors@R": "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"), email = \"deepayan.sarkar@r-project.org\", comment = c(ORCID = \"0000-0003-4107-1553\")), person(\"Felix\", \"Andrews\", role = \"ctb\"), person(\"Kevin\", \"Wright\", role = \"ctb\", comment = \"documentation\"), person(\"Neil\", \"Klepeis\", role = \"ctb\"), person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous improvements\"), person(\"Zhijian (Jason)\", \"Wen\", role = \"cph\", comment = \"filled contour code\"), person(\"Paul\", \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"), person(\"Stefan\", \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"), person(\"Achim\", \"Zeileis\", role = \"ctb\", comment = \"modern colors\"), person(\"Alexandre\", \"Courtiol\", role = \"ctb\", comment = \"generics for larrows, lpolygon, lrect and lsegments\") )", + "Description": "A powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements. See ?Lattice for an introduction.", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "KernSmooth", + "MASS", + "latticeExtra", + "colorspace" + ], + "Imports": [ + "grid", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Enhances": [ + "chron", + "zoo" + ], + "LazyLoad": "yes", + "LazyData": "yes", + "License": "GPL (>= 2)", + "URL": "https://lattice.r-forge.r-project.org/", + "BugReports": "https://github.com/deepayan/lattice/issues", + "NeedsCompilation": "yes", + "Author": "Deepayan Sarkar [aut, cre] (), Felix Andrews [ctb], Kevin Wright [ctb] (documentation), Neil Klepeis [ctb], Johan Larsson [ctb] (miscellaneous improvements), Zhijian (Jason) Wen [cph] (filled contour code), Paul Murrell [ctb], Stefan Eng [ctb] (violin plot improvements), Achim Zeileis [ctb] (modern colors), Alexandre Courtiol [ctb] (generics for larrows, lpolygon, lrect and lsegments)", + "Maintainer": "Deepayan Sarkar ", + "Repository": "CRAN" + }, + "lazyeval": { + "Package": "lazyeval", + "Version": "0.2.2", + "Source": "Repository", + "Title": "Lazy (Non-Standard) Evaluation", + "Description": "An alternative approach to non-standard evaluation using formulas. Provides a full implementation of LISP style 'quasiquotation', making it easier to generate code with other code.", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", ,\"hadley@rstudio.com\", c(\"aut\", \"cre\")), person(\"RStudio\", role = \"cph\") )", + "License": "GPL-3", + "LazyData": "true", + "Depends": [ + "R (>= 3.1.0)" + ], + "Suggests": [ + "knitr", + "rmarkdown (>= 0.2.65)", + "testthat", + "covr" + ], + "VignetteBuilder": "knitr", + "RoxygenNote": "6.1.1", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], RStudio [cph]", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "leafem": { + "Package": "leafem", + "Version": "0.2.3", + "Source": "Repository", + "Title": "'leaflet' Extensions for 'mapview'", + "Authors@R": "c(person(given = \"Tim\", family = \"Appelhans\", role = c(\"cre\", \"aut\"), email = \"tim.appelhans@gmail.com\"), person(given = \"Christoph\", family = \"Reudenbach\", role = \"ctb\", email = \"reudenbach@geo.uni-marburg.de\"), person(given = \"Kenton\", family = \"Russell\", role = \"ctb\"), person(given = \"Jochen\", family = \"Darley\", role = \"ctb\", email = \"Debugger@jedimasters.de\"), person(given = \"Daniel\", family = \"Montague\", role = c(\"ctb\", \"cph\"), comment = \"Leaflet.EasyButton plugin\"), person(given = \"Lorenzo\", family = \"Busetto\", role = c(\"ctb\"), email = \"lbusett@gmail.com\"), person(given = \"Luigi\", family = \"Ranghetti\", role = c(\"ctb\")), person(given = \"Miles\", family = \"McBain\", role = c(\"ctb\")), person(given = \"Sebastian\", family = \"Gatscha\", role = \"ctb\", email = \"sebastian_gatscha@gmx.at\"), person(given = \"Björn\", family = \"Harrtell\", role = c(\"ctb\", \"cph\"), comment = \"FlatGeobuf plugin\"), person(given = \"Daniel\", family = \"Dufour\", role = c(\"ctb\", \"cph\"), comment = \"georaster-layer-for-leaflet\"), person(given = \"Yeedle\", family = \"Neuwirth\", role = \"ctb\"), person(given = \"Derek\", family = \"Friend\", role = \"ctb\", email = \"dafriend.r@gmail.com\"), person(given = \"Kevin\", family = \"Cazelles\", role = \"ctb\", email = \"kevin.cazelles@gmail.com\", comment = c(ORCID = \"0000-0001-6619-9874\")))", + "Maintainer": "Tim Appelhans ", + "Description": "Provides extensions for packages 'leaflet' & 'mapdeck', many of which are used by package 'mapview'. Focus is on functionality readily available in Geographic Information Systems such as 'Quantum GIS'. Includes functions to display coordinates of mouse pointer position, query image values via mouse pointer and zoom-to-layer buttons. Additionally, provides a feature type agnostic function to add points, lines, polygons to a map.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-spatial/leafem, https://r-spatial.github.io/leafem/", + "BugReports": "https://github.com/r-spatial/leafem/issues", + "Depends": [ + "R (>= 3.1.0)" + ], + "Imports": [ + "base64enc", + "geojsonsf", + "htmltools (>= 0.3)", + "htmlwidgets", + "leaflet (>= 2.0.1)", + "methods", + "raster", + "sf", + "png" + ], + "Suggests": [ + "clipr", + "leafgl", + "lwgeom", + "mapdeck", + "plainview", + "stars" + ], + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Tim Appelhans [cre, aut], Christoph Reudenbach [ctb], Kenton Russell [ctb], Jochen Darley [ctb], Daniel Montague [ctb, cph] (Leaflet.EasyButton plugin), Lorenzo Busetto [ctb], Luigi Ranghetti [ctb], Miles McBain [ctb], Sebastian Gatscha [ctb], Björn Harrtell [ctb, cph] (FlatGeobuf plugin), Daniel Dufour [ctb, cph] (georaster-layer-for-leaflet), Yeedle Neuwirth [ctb], Derek Friend [ctb], Kevin Cazelles [ctb] ()", + "Repository": "RSPM" + }, + "leaflet": { + "Package": "leaflet", + "Version": "2.2.2", + "Source": "Repository", + "Type": "Package", + "Title": "Create Interactive Web Maps with the JavaScript 'Leaflet' Library", + "Authors@R": "c( person(\"Joe\", \"Cheng\", , \"joe@posit.co\", role = c(\"aut\", \"cre\")), person(\"Barret\", \"Schloerke\", , \"barret@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0001-9986-114X\")), person(\"Bhaskar\", \"Karambelkar\", role = \"aut\"), person(\"Yihui\", \"Xie\", role = \"aut\"), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Kenton\", \"Russell\", role = \"ctb\"), person(\"Kent\", \"Johnson\", role = \"ctb\"), person(\"Vladimir\", \"Agafonkin\", role = c(\"ctb\", \"cph\"), comment = \"Leaflet library\"), person(\"CloudMade\", role = \"cph\", comment = \"Leaflet library\"), person(\"Leaflet contributors\", role = \"ctb\", comment = \"Leaflet library\"), person(\"Brandon Copeland\", role = c(\"ctb\", \"cph\"), comment = \"leaflet-measure plugin\"), person(\"Joerg Dietrich\", role = c(\"ctb\", \"cph\"), comment = \"Leaflet.Terminator plugin\"), person(\"Benjamin Becquet\", role = c(\"ctb\", \"cph\"), comment = \"Leaflet.MagnifyingGlass plugin\"), person(\"Norkart AS\", role = c(\"ctb\", \"cph\"), comment = \"Leaflet.MiniMap plugin\"), person(\"L. 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A class representing multiple lower triangular matrices and corresponding methods are part of this package.", + "Imports": [ + "stats" + ], + "Depends": [ + "R(>= 3.5.0)" + ], + "Suggests": [ + "qrng", + "numDeriv" + ], + "License": "GPL-2", + "URL": "http://mvtnorm.R-forge.R-project.org", + "NeedsCompilation": "yes", + "Author": "Alan Genz [aut], Frank Bretz [aut], Tetsuhisa Miwa [aut], Xuefei Mi [aut], Friedrich Leisch [ctb], Fabian Scheipl [ctb], Bjoern Bornkamp [ctb] (), Martin Maechler [ctb] (), Torsten Hothorn [aut, cre] ()", + "Maintainer": "Torsten Hothorn ", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-164", + "Source": "Repository", + "Date": "2023-11-27", + "Priority": "recommended", + "Title": "Linear and Nonlinear Mixed Effects Models", + "Authors@R": "c(person(\"José\", \"Pinheiro\", role = \"aut\", comment = \"S version\"), person(\"Douglas\", \"Bates\", role = \"aut\", comment = \"up to 2007\"), person(\"Saikat\", \"DebRoy\", role = \"ctb\", comment = \"up to 2002\"), person(\"Deepayan\", \"Sarkar\", role = \"ctb\", comment = \"up to 2005\"), person(\"EISPACK authors\", role = \"ctb\", comment = \"src/rs.f\"), person(\"Siem\", \"Heisterkamp\", role = \"ctb\", comment = \"Author fixed sigma\"), person(\"Bert\", \"Van Willigen\",role = \"ctb\", comment = \"Programmer fixed sigma\"), person(\"Johannes\", \"Ranke\", role = \"ctb\", comment = \"varConstProp()\"), person(\"R Core Team\", email = \"R-core@R-project.org\", role = c(\"aut\", \"cre\")))", + "Contact": "see 'MailingList'", + "Description": "Fit and compare Gaussian linear and nonlinear mixed-effects models.", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "graphics", + "stats", + "utils", + "lattice" + ], + "Suggests": [ + "Hmisc", + "MASS", + "SASmixed" + ], + "LazyData": "yes", + "Encoding": "UTF-8", + "License": "GPL (>= 2)", + "BugReports": "https://bugs.r-project.org", + "MailingList": "R-help@r-project.org", + "URL": "https://svn.r-project.org/R-packages/trunk/nlme/", + "NeedsCompilation": "yes", + "Author": "José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), Johannes Ranke [ctb] (varConstProp()), R Core Team [aut, cre]", + "Maintainer": "R Core Team ", + "Repository": "RSPM" + }, + "nloptr": { + "Package": "nloptr", + "Version": "2.1.1", + "Source": "Repository", + "Type": "Package", + "Title": "R Interface to NLopt", + "Authors@R": "c(person(\"Jelmer\", \"Ypma\", role = \"aut\", email = \"uctpjyy@ucl.ac.uk\"), person(c(\"Steven\", \"G.\"), \"Johnson\", role = \"aut\", comment = \"author of the NLopt C library\"), person(\"Aymeric\", \"Stamm\", role = c(\"ctb\", \"cre\"), email = \"aymeric.stamm@cnrs.fr\", comment = c(ORCID = \"0000-0002-8725-3654\")), person(c(\"Hans\", \"W.\"), \"Borchers\", role = \"ctb\", email = \"hwborchers@googlemail.com\"), person(\"Dirk\", \"Eddelbuettel\", role = \"ctb\", email = \"edd@debian.org\"), person(\"Brian\", \"Ripley\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Kurt\", \"Hornik\", role = \"ctb\", comment = \"build process on multiple OS\"), person(\"Julien\", \"Chiquet\", role = \"ctb\"), person(\"Avraham\", \"Adler\", role = \"ctb\", email = \"Avraham.Adler@gmail.com\", comment = c(ORCID = \"0000-0002-3039-0703\")), person(\"Xiongtao\", \"Dai\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\", email = \"jeroen@berkeley.edu\"))", + "Description": "Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.", + "License": "LGPL (>= 3)", + "SystemRequirements": "cmake (>= 3.2.0) which is used only on Linux or macOS systems when no system build of nlopt (>= 2.7.0) can be found.", + "Biarch": "true", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Suggests": [ + "knitr", + "rmarkdown", + "covr", + "tinytest" + ], + "VignetteBuilder": "knitr", + "URL": "https://github.com/astamm/nloptr, https://astamm.github.io/nloptr/", + "BugReports": "https://github.com/astamm/nloptr/issues", + "NeedsCompilation": "yes", + "Author": "Jelmer Ypma [aut], Steven G. Johnson [aut] (author of the NLopt C library), Aymeric Stamm [ctb, cre] (), Hans W. Borchers [ctb], Dirk Eddelbuettel [ctb], Brian Ripley [ctb] (build process on multiple OS), Kurt Hornik [ctb] (build process on multiple OS), Julien Chiquet [ctb], Avraham Adler [ctb] (), Xiongtao Dai [ctb], Jeroen Ooms [ctb]", + "Maintainer": "Aymeric Stamm ", + "Repository": "RSPM" + }, + "nnet": { + "Package": "nnet", + "Version": "7.3-19", + "Source": "Repository", + "Priority": "recommended", + "Date": "2023-05-02", + "Depends": [ + "R (>= 3.0.0)", + "stats", + "utils" + ], + "Suggests": [ + "MASS" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"William\", \"Venables\", role = \"cph\"))", + "Description": "Software for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.", + "Title": "Feed-Forward Neural Networks and Multinomial Log-Linear Models", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], William Venables [cph]", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" + }, + "numDeriv": { + "Package": "numDeriv", + "Version": "2016.8-1.1", + "Source": "Repository", + "Title": "Accurate Numerical Derivatives", + "Description": "Methods for calculating (usually) accurate numerical first and second order derivatives. Accurate calculations are done using 'Richardson''s' extrapolation or, when applicable, a complex step derivative is available. A simple difference method is also provided. Simple difference is (usually) less accurate but is much quicker than 'Richardson''s' extrapolation and provides a useful cross-check. Methods are provided for real scalar and vector valued functions.", + "Depends": [ + "R (>= 2.11.1)" + ], + "LazyLoad": "yes", + "ByteCompile": "yes", + "License": "GPL-2", + "Copyright": "2006-2011, Bank of Canada. 2012-2016, Paul Gilbert", + "Author": "Paul Gilbert and Ravi Varadhan", + "Maintainer": "Paul Gilbert ", + "URL": "http://optimizer.r-forge.r-project.org/", + "NeedsCompilation": "no", + "Repository": "RSPM", + "Encoding": "UTF-8" + }, + "openssl": { + "Package": "openssl", + "Version": "2.2.2", + "Source": "Repository", + "Type": "Package", + "Title": "Toolkit for Encryption, Signatures and Certificates Based on OpenSSL", + "Authors@R": "c(person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Oliver\", \"Keyes\", role = \"ctb\"))", + "Description": "Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.", + "License": "MIT + file LICENSE", + "URL": "https://jeroen.r-universe.dev/openssl", + "BugReports": "https://github.com/jeroen/openssl/issues", + "SystemRequirements": "OpenSSL >= 1.0.2", + "VignetteBuilder": "knitr", + "Imports": [ + "askpass" + ], + "Suggests": [ + "curl", + "testthat (>= 2.1.0)", + "digest", + "knitr", + "rmarkdown", + "jsonlite", + "jose", + "sodium" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Oliver Keyes [ctb]", + "Maintainer": "Jeroen Ooms ", + "Repository": "RSPM" + }, + "openxlsx": { + "Package": "openxlsx", + "Version": "4.2.7.1", + "Source": "Repository", + "Type": "Package", + "Title": "Read, Write and Edit xlsx Files", + "Date": "2024-09-19", + "Authors@R": "c(person(given = \"Philipp\", family = \"Schauberger\", role = \"aut\", email = \"philipp@schauberger.co.at\"), person(given = \"Alexander\", family = \"Walker\", role = \"aut\", email = \"Alexander.Walker1989@gmail.com\"), person(given = \"Luca\", family = \"Braglia\", role = \"ctb\"), person(given = \"Joshua\", family = \"Sturm\", role = \"ctb\"), person(given = \"Jan Marvin\", family = \"Garbuszus\", role = c(\"ctb\", \"cre\"), email = \"jan.garbuszus@ruhr-uni-bochum.de\"), person(given = \"Jordan Mark\", family = \"Barbone\", role = \"ctb\", email = \"jmbarbone@gmail.com\", comment = c(ORCID = \"0000-0001-9788-3628\")), person(given = \"David\", family = \"Zimmermann\", role = \"ctb\", email = \"david_j_zimmermann@hotmail.com\"), person(given = \"Reinhold\", family = \"Kainhofer\", role = \"ctb\", email = \"reinhold@kainhofer.com\"))", + "Description": "Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java.", + "License": "MIT + file LICENSE", + "URL": "https://ycphs.github.io/openxlsx/index.html, https://github.com/ycphs/openxlsx", + "BugReports": "https://github.com/ycphs/openxlsx/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "grDevices", + "methods", + "Rcpp", + "stats", + "stringi", + "utils", + "zip" + ], + "Suggests": [ + "curl", + "formula.tools", + "knitr", + "rmarkdown", + "testthat" + ], + "LinkingTo": [ + "Rcpp" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.3.2", + "Collate": "'CommentClass.R' 'HyperlinkClass.R' 'RcppExports.R' 'class_definitions.R' 'StyleClass.R' 'WorkbookClass.R' 'asserts.R' 'baseXML.R' 'borderFunctions.R' 'build_workbook.R' 'chartsheet_class.R' 'conditional_formatting.R' 'data-fontSizeLookupTables.R' 'helperFunctions.R' 'loadWorkbook.R' 'onUnload.R' 'openXL.R' 'openxlsx-package.R' 'openxlsx.R' 'openxlsxCoerce.R' 'readWorkbook.R' 'setWindowSize.R' 'sheet_data_class.R' 'utils.R' 'workbook_column_widths.R' 'workbook_read_workbook.R' 'workbook_write_data.R' 'worksheet_class.R' 'wrappers.R' 'writeData.R' 'writeDataTable.R' 'writexlsx.R' 'zzz.R'", + "LazyData": "true", + "NeedsCompilation": "yes", + "Author": "Philipp Schauberger [aut], Alexander Walker [aut], Luca Braglia [ctb], Joshua Sturm [ctb], Jan Marvin Garbuszus [ctb, cre], Jordan Mark Barbone [ctb] (), David Zimmermann [ctb], Reinhold Kainhofer [ctb]", + "Maintainer": "Jan Marvin Garbuszus ", + "Repository": "RSPM" + }, + "pagedown": { + "Package": "pagedown", + "Version": "0.21", + "Source": "Repository", + "Type": "Package", + "Title": "Paginate the HTML Output of R Markdown with CSS for Print", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Romain\", \"Lesur\", role = c(\"aut\", \"cph\"), comment = c(ORCID = \"0000-0002-0721-5595\")), person(\"Christophe\", \"Dervieux\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Brent\", \"Thorne\", role = \"aut\", comment = c(ORCID = \"0000-0002-1099-3857\")), person(\"Xianying\", \"Tan\", role = \"aut\", comment = c(ORCID = \"0000-0002-6072-3521\")), person(\"Atsushi\", \"Yasumoto\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0002-8335-495X\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Adam\", \"Hyde\", role = \"ctb\", comment = \"paged.js in resources/js/\"), person(\"Min-Zhong\", \"Lu\", role = \"ctb\", comment = \"resume.css in resources/css/\"), person(\"Zulko\", role = \"ctb\", comment = \"poster-relaxed.css in resources/css/\"), person() )", + "Description": "Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "rmarkdown (>= 2.13)", + "bookdown (>= 0.8)", + "htmltools", + "jsonlite", + "later (>= 1.0.0)", + "processx", + "servr (>= 0.31)", + "httpuv", + "xfun", + "websocket" + ], + "Suggests": [ + "promises", + "testit", + "xaringan", + "pdftools", + "revealjs", + "covr", + "xml2" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/pagedown", + "BugReports": "https://github.com/rstudio/pagedown/issues", + "SystemRequirements": "Pandoc (>= 2.2.3)", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Romain Lesur [aut, cph] (), Christophe Dervieux [ctb] (), Brent Thorne [aut] (), Xianying Tan [aut] (), Atsushi Yasumoto [ctb] (), Posit Software, PBC [cph, fnd], Adam Hyde [ctb] (paged.js in resources/js/), Min-Zhong Lu [ctb] (resume.css in resources/css/), Zulko [ctb] (poster-relaxed.css in resources/css/)", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" + }, + "parsedate": { + "Package": "parsedate", + "Version": "1.3.1", + "Source": "Repository", + "Title": "Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats", + "Maintainer": "Gábor Csárdi ", + "Author": "Gábor Csárdi, Linus Torvalds", + "Description": "Parse dates automatically, without the need of specifying a format. Currently it includes the git date parser. It can also recognize and parse all ISO 8601 formats.", + "License": "GPL-2", + "Suggests": [ + "covr", + "testthat", + "withr" + ], + "URL": "https://github.com/gaborcsardi/parsedate", + "BugReports": "https://github.com/gaborcsardi/parsedate/issues", + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Repository": "RSPM" + }, + "pbkrtest": { + "Package": "pbkrtest", + "Version": "0.5.3", + "Source": "Repository", + "Title": "Parametric Bootstrap, Kenward-Roger and Satterthwaite Based Methods for Test in Mixed Models", + "Authors@R": "c( person(given = \"Ulrich\", family = \"Halekoh\", email = \"uhalekoh@health.sdu.dk\", role = c(\"aut\", \"cph\")), person(given = \"Søren\", family = \"Højsgaard\", email = \"sorenh@math.aau.dk\", role = c(\"aut\", \"cre\", \"cph\")) )", + "Maintainer": "Søren Højsgaard ", + "Description": "Computes p-values based on (a) Satterthwaite or Kenward-Rogers degree of freedom methods and (b) parametric bootstrap for mixed effects models as implemented in the 'lme4' package. Implements parametric bootstrap test for generalized linear mixed models as implemented in 'lme4' and generalized linear models. The package is documented in the paper by Halekoh and Højsgaard, (2012, ). Please see 'citation(\"pbkrtest\")' for citation details.", + "URL": "https://people.math.aau.dk/~sorenh/software/pbkrtest/", + "Depends": [ + "R (>= 4.2.0)", + "lme4 (>= 1.1.31)" + ], + "Imports": [ + "broom", + "dplyr", + "MASS", + "methods", + "numDeriv", + "Matrix (>= 1.2.3)", + "doBy" + ], + "Suggests": [ + "markdown", + "knitr" + ], + "Encoding": "UTF-8", + "VignetteBuilder": "knitr", + "License": "GPL (>= 2)", + "ByteCompile": "Yes", + "RoxygenNote": "7.3.1", + "LazyData": "true", + "NeedsCompilation": "no", + "Author": "Ulrich Halekoh [aut, cph], Søren Højsgaard [aut, cre, cph]", + "Repository": "RSPM" + }, + "pillar": { + "Package": "pillar", + "Version": "1.9.0", + "Source": "Repository", + "Title": "Coloured Formatting for Columns", + "Authors@R": "c(person(given = \"Kirill\", family = \"M\\u00fcller\", role = c(\"aut\", \"cre\"), email = \"kirill@cynkra.com\", comment = c(ORCID = \"0000-0002-1416-3412\")), person(given = \"Hadley\", family = \"Wickham\", role = \"aut\"), person(given = \"RStudio\", role = \"cph\"))", + "Description": "Provides 'pillar' and 'colonnade' generics designed for formatting columns of data using the full range of colours provided by modern terminals.", + "License": "MIT + file LICENSE", + "URL": "https://pillar.r-lib.org/, https://github.com/r-lib/pillar", + "BugReports": "https://github.com/r-lib/pillar/issues", + "Imports": [ + "cli (>= 2.3.0)", + "fansi", + "glue", + "lifecycle", + "rlang (>= 1.0.2)", + "utf8 (>= 1.1.0)", + "utils", + "vctrs (>= 0.5.0)" + ], + "Suggests": [ + "bit64", + "DBI", + "debugme", + "DiagrammeR", + "dplyr", + "formattable", + "ggplot2", + "knitr", + "lubridate", + "nanotime", + "nycflights13", + "palmerpenguins", + "rmarkdown", + "scales", + "stringi", + "survival", + "testthat (>= 3.1.1)", + "tibble", + "units (>= 0.7.2)", + "vdiffr", + "withr" + ], + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "true", + "Config/testthat/start-first": "format_multi_fuzz, format_multi_fuzz_2, format_multi, ctl_colonnade, ctl_colonnade_1, ctl_colonnade_2", + "Config/autostyle/scope": "line_breaks", + "Config/autostyle/strict": "true", + "Config/gha/extra-packages": "DiagrammeR=?ignore-before-r=3.5.0", + "Config/Needs/website": "tidyverse/tidytemplate", + "NeedsCompilation": "no", + "Author": "Kirill Müller [aut, cre] (), Hadley Wickham [aut], RStudio [cph]", + "Maintainer": "Kirill Müller ", + "Repository": "RSPM" + }, + "pkgconfig": { + "Package": "pkgconfig", + "Version": "2.0.3", + "Source": "Repository", + "Title": "Private Configuration for 'R' Packages", + "Author": "Gábor Csárdi", + "Maintainer": "Gábor Csárdi ", + "Description": "Set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.", + "License": "MIT + file LICENSE", + "LazyData": "true", + "Imports": [ + "utils" + ], + "Suggests": [ + "covr", + "testthat", + "disposables (>= 1.0.3)" + ], + "URL": "https://github.com/r-lib/pkgconfig#readme", + "BugReports": "https://github.com/r-lib/pkgconfig/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "RSPM" + }, + "plyr": { + "Package": "plyr", + "Version": "1.8.9", + "Source": "Repository", + "Title": "Tools for Splitting, Applying and Combining Data", + "Authors@R": "person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", role = c(\"aut\", \"cre\"))", + "Description": "A set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. 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'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).", + "License": "GPL (>= 3)", + "URL": "https://rspatial.org/, https://rspatial.github.io/terra/", + "BugReports": "https://github.com/rspatial/terra/issues/", + "LazyLoad": "yes", + "Authors@R": "c( person(\"Robert J.\", \"Hijmans\", role = c(\"cre\", \"aut\"), email = \"r.hijmans@gmail.com\", comment = c(ORCID = \"0000-0001-5872-2872\")), person(\"Roger\", \"Bivand\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2392-6140\")), person(\"Krzysztof\", \"Dyba\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8614-3816\")), person(\"Edzer\", \"Pebesma\", role = \"ctb\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(\"Michael D.\", \"Sumner\", role = \"ctb\"))", + "NeedsCompilation": "yes", + "Author": "Robert J. Hijmans [cre, aut] (), Roger Bivand [ctb] (), Krzysztof Dyba [ctb] (), Edzer Pebesma [ctb] (), Michael D. 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Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "RSPM" + }, + "wk": { + "Package": "wk", + "Version": "0.9.4", + "Source": "Repository", + "Title": "Lightweight Well-Known Geometry Parsing", + "Authors@R": "c( person(given = \"Dewey\", family = \"Dunnington\", role = c(\"aut\", \"cre\"), email = \"dewey@fishandwhistle.net\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(given = \"Edzer\", family = \"Pebesma\", role = c(\"aut\"), email = \"edzer.pebesma@uni-muenster.de\", comment = c(ORCID = \"0000-0001-8049-7069\")), person(given = \"Anthony\", family = \"North\", email = \"anthony.jl.north@gmail.com\", role = c(\"ctb\")) )", + "Maintainer": "Dewey Dunnington ", + "Description": "Provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse; well-known text is human-readable and is useful for writing tests. These formats are useful in R only if the information they contain can be accessed in R, for which high-performance functions are provided here.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "Suggests": [ + "testthat (>= 3.0.0)", + "vctrs (>= 0.3.0)", + "sf", + "tibble", + "readr" + ], + "URL": "https://paleolimbot.github.io/wk/, https://github.com/paleolimbot/wk", + "BugReports": "https://github.com/paleolimbot/wk/issues", + "Config/testthat/edition": "3", + "Depends": [ + "R (>= 2.10)" + ], + "LazyData": "true", + "NeedsCompilation": "yes", + "Author": "Dewey Dunnington [aut, cre] (), Edzer Pebesma [aut] (), Anthony North [ctb]", + "Repository": "RSPM" + }, + "xaringan": { + "Package": "xaringan", + "Version": "0.30", + "Source": "Repository", + "Type": "Package", + "Title": "Presentation Ninja", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), # contributors ordered alphabetically below person(\"Alessandro\", \"Gasparini\", role = \"ctb\", comment = c(ORCID = \"0000-0002-8319-7624\")), person(\"Benjie\", \"Gillam\", role = \"ctb\"), person(\"Claus Thorn\", \"Ekstrøm\", role = \"ctb\"), person(\"Daniel\", \"Anderson\", role = \"ctb\"), person(\"Dawei\", \"Lang\", role = \"ctb\"), person(\"Deo\", \"Salil\", role = \"ctb\"), person(\"Emi\", \"Tanaka\", role = \"ctb\"), person(\"Garrick\", \"Aden-Buie\", role = \"ctb\", comment = c(ORCID = \"0000-0002-7111-0077\")), person(\"Iñaki\", \"Ucar\", role = \"ctb\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"John\", \"Little\", role = \"ctb\"), person(\"Joselyn\", \"Chávez\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4974-4591\")), person(\"Joseph\", \"Casillas\", role = \"ctb\"), person(\"JooYoung\", \"Seo\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4064-6012\")), person(\"Lucy\", \"D'Agostino McGowan\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7297-9359\")), person(\"Malcolm\", \"Barrett\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0299-5825\")), person(c(\"Matthew\", \"Mark\"), \"Strasiotto\", role = \"ctb\", comment = c(github = \"mstr3336\")), person(\"Michael Wayne\", \"Kearney\", role = \"ctb\"), person(\"Nan-Hung\", \"Hsieh\", role = \"ctb\"), person(\"Ole Petter\", \"Bang\", role = \"ctb\", comment = \"CSS in rmarkdown/templates/xaringan/resources/default.css\"), person(\"Orlando\", \"Olaya Bucaro\", role = \"ctb\"), person(\"Patrick\", \"Schratz\", role = \"ctb\"), person(\"Paul\", \"Klemm\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5985-1737\")), person(\"Paul\", \"Lemmens\", role = \"ctb\"), person(\"Robert\", \"Fromont\", role = \"ctb\", email = \"robert.fromont@canterbury.ac.nz\", comment = c(ORCID = \"0000-0001-5271-5487\")), person(\"Sean\", \"Lopp\", role = \"ctb\"), person(\"Silvia\", \"Canelon\", role = \"ctb\", comment = c(ORCID = \"0000-0003-1709-1394\")), person(\"Susan\", \"VanderPlas\", role = \"ctb\", comment = c(ORCID = \"0000-0002-3803-0972\")), person(\"Tuo\", \"Wang\", role = \"ctb\"), person(\"Waldir\", \"Leoncio\", role = \"ctb\", email = \"w.l.netto@medisin.uio.no\"), person(\"Yongfu\", \"Liao\", role = \"ctb\"), person(\"Yue\", \"Jiang\", role = \"ctb\", comment = c(ORCID = \"0000-0002-9798-5517\")), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = c(\"ctb\"), email = \"zkamvar@gmail.com\", comment = c(ORCID = \"0000-0003-1458-7108\")), person() )", + "Description": "Create HTML5 slides with R Markdown and the JavaScript library 'remark.js' ().", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "htmltools", + "knitr (>= 1.30)", + "servr (>= 0.30)", + "xfun (>= 0.18)", + "rmarkdown (>= 2.8)" + ], + "Suggests": [ + "rstudioapi", + "jsonlite", + "testit" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xaringan", + "BugReports": "https://github.com/yihui/xaringan/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre] (), Posit Software, PBC [cph, fnd], Alessandro Gasparini [ctb] (), Benjie Gillam [ctb], Claus Thorn Ekstrøm [ctb], Daniel Anderson [ctb], Dawei Lang [ctb], Deo Salil [ctb], Emi Tanaka [ctb], Garrick Aden-Buie [ctb] (), Iñaki Ucar [ctb] (), John Little [ctb], Joselyn Chávez [ctb] (), Joseph Casillas [ctb], JooYoung Seo [ctb] (), Lucy D'Agostino McGowan [ctb] (), Malcolm Barrett [ctb] (), Matthew Mark Strasiotto [ctb] (mstr3336), Michael Wayne Kearney [ctb], Nan-Hung Hsieh [ctb], Ole Petter Bang [ctb] (CSS in rmarkdown/templates/xaringan/resources/default.css), Orlando Olaya Bucaro [ctb], Patrick Schratz [ctb], Paul Klemm [ctb] (), Paul Lemmens [ctb], Robert Fromont [ctb] (), Sean Lopp [ctb], Silvia Canelon [ctb] (), Susan VanderPlas [ctb] (), Tuo Wang [ctb], Waldir Leoncio [ctb], Yongfu Liao [ctb], Yue Jiang [ctb] (), Zhian N. Kamvar [ctb] ()", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" + }, + "xfun": { + "Package": "xfun", + "Version": "0.48", + "Source": "Repository", + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ + "grDevices", + "stats", + "tools" + ], + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown", + "knitr (>= 1.47)", + "remotes", + "pak", + "rhub", + "renv", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs", + "rmarkdown" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "RSPM" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org/, https://github.com/r-lib/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "cli", + "methods", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Hadley Wickham ", + "Repository": "RSPM" + }, + "xmlparsedata": { + "Package": "xmlparsedata", + "Version": "1.0.5", + "Source": "Repository", + "Title": "Parse Data of 'R' Code as an 'XML' Tree", + "Author": "Gábor Csárdi", + "Maintainer": "Gábor Csárdi ", + "Description": "Convert the output of 'utils::getParseData()' to an 'XML' tree, that one can search via 'XPath', and easier to manipulate in general.", + "License": "MIT + file LICENSE", + "LazyData": "true", + "URL": "https://github.com/r-lib/xmlparsedata#readme", + "BugReports": "https://github.com/r-lib/xmlparsedata/issues", + "RoxygenNote": "6.0.1", + "Suggests": [ + "covr", + "testthat", + "xml2" + ], + "Depends": [ + "R (>= 3.0.0)" + ], + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Repository": "RSPM" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Date": "2019-04-08", + "Title": "Export Tables to LaTeX or HTML", + "Authors@R": "c(person(\"David B.\", \"Dahl\", role=\"aut\"), person(\"David\", \"Scott\", role=c(\"aut\",\"cre\"), email=\"d.scott@auckland.ac.nz\"), person(\"Charles\", \"Roosen\", role=\"aut\"), person(\"Arni\", \"Magnusson\", role=\"aut\"), person(\"Jonathan\", \"Swinton\", role=\"aut\"), person(\"Ajay\", \"Shah\", role=\"ctb\"), person(\"Arne\", \"Henningsen\", role=\"ctb\"), person(\"Benno\", \"Puetz\", role=\"ctb\"), person(\"Bernhard\", \"Pfaff\", role=\"ctb\"), person(\"Claudio\", \"Agostinelli\", role=\"ctb\"), person(\"Claudius\", \"Loehnert\", role=\"ctb\"), person(\"David\", \"Mitchell\", role=\"ctb\"), person(\"David\", \"Whiting\", role=\"ctb\"), person(\"Fernando da\", \"Rosa\", role=\"ctb\"), person(\"Guido\", \"Gay\", role=\"ctb\"), person(\"Guido\", \"Schulz\", role=\"ctb\"), person(\"Ian\", \"Fellows\", role=\"ctb\"), person(\"Jeff\", \"Laake\", role=\"ctb\"), person(\"John\", \"Walker\", role=\"ctb\"), person(\"Jun\", \"Yan\", role=\"ctb\"), person(\"Liviu\", \"Andronic\", role=\"ctb\"), person(\"Markus\", \"Loecher\", role=\"ctb\"), person(\"Martin\", \"Gubri\", role=\"ctb\"), person(\"Matthieu\", \"Stigler\", role=\"ctb\"), person(\"Robert\", \"Castelo\", role=\"ctb\"), person(\"Seth\", \"Falcon\", role=\"ctb\"), person(\"Stefan\", \"Edwards\", role=\"ctb\"), person(\"Sven\", \"Garbade\", role=\"ctb\"), person(\"Uwe\", \"Ligges\", role=\"ctb\"))", + "Maintainer": "David Scott ", + "Imports": [ + "stats", + "utils" + ], + "Suggests": [ + "knitr", + "plm", + "zoo", + "survival" + ], + "VignetteBuilder": "knitr", + "Description": "Coerce data to LaTeX and HTML tables.", + "URL": "http://xtable.r-forge.r-project.org/", + "Depends": [ + "R (>= 2.10.0)" + ], + "License": "GPL (>= 2)", + "Repository": "RSPM", + "NeedsCompilation": "no", + "Author": "David B. Dahl [aut], David Scott [aut, cre], Charles Roosen [aut], Arni Magnusson [aut], Jonathan Swinton [aut], Ajay Shah [ctb], Arne Henningsen [ctb], Benno Puetz [ctb], Bernhard Pfaff [ctb], Claudio Agostinelli [ctb], Claudius Loehnert [ctb], David Mitchell [ctb], David Whiting [ctb], Fernando da Rosa [ctb], Guido Gay [ctb], Guido Schulz [ctb], Ian Fellows [ctb], Jeff Laake [ctb], John Walker [ctb], Jun Yan [ctb], Liviu Andronic [ctb], Markus Loecher [ctb], Martin Gubri [ctb], Matthieu Stigler [ctb], Robert Castelo [ctb], Seth Falcon [ctb], Stefan Edwards [ctb], Sven Garbade [ctb], Uwe Ligges [ctb]", + "Encoding": "UTF-8" + }, + "xts": { + "Package": "xts", + "Version": "0.14.1", + "Source": "Repository", + "Type": "Package", + "Title": "eXtensible Time Series", + "Authors@R": "c( person(given=c(\"Jeffrey\",\"A.\"), family=\"Ryan\", role=c(\"aut\",\"cph\")), person(given=c(\"Joshua\",\"M.\"), family=\"Ulrich\", role=c(\"cre\",\"aut\"), email=\"josh.m.ulrich@gmail.com\"), person(given=\"Ross\", family=\"Bennett\", role=\"ctb\"), person(given=\"Corwin\", family=\"Joy\", role=\"ctb\") )", + "Depends": [ + "R (>= 3.6.0)", + "zoo (>= 1.7-12)" + ], + "Imports": [ + "methods" + ], + "LinkingTo": [ + "zoo" + ], + "Suggests": [ + "timeSeries", + "timeDate", + "tseries", + "chron", + "tinytest" + ], + "LazyLoad": "yes", + "Description": "Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.", + "License": "GPL (>= 2)", + "URL": "https://joshuaulrich.github.io/xts/, https://github.com/joshuaulrich/xts", + "BugReports": "https://github.com/joshuaulrich/xts/issues", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Jeffrey A. Ryan [aut, cph], Joshua M. Ulrich [cre, aut], Ross Bennett [ctb], Corwin Joy [ctb]", + "Maintainer": "Joshua M. Ulrich ", + "Repository": "RSPM" + }, + "yaml": { + "Package": "yaml", + "Version": "2.3.10", + "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", + "Repository": "CRAN", + "Encoding": "UTF-8" + }, + "zip": { + "Package": "zip", + "Version": "2.3.1", + "Source": "Repository", + "Title": "Cross-Platform 'zip' Compression", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kuba\", \"Podgórski\", role = \"ctb\"), person(\"Rich\", \"Geldreich\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Cross-Platform 'zip' Compression Library. A replacement for the 'zip' function, that does not require any additional external tools on any platform.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/r-lib/zip, https://r-lib.github.io/zip/", + "BugReports": "https://github.com/r-lib/zip/issues", + "Suggests": [ + "covr", + "processx", + "R6", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Gábor Csárdi [aut, cre], Kuba Podgórski [ctb], Rich Geldreich [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "RSPM" + }, + "zoo": { + "Package": "zoo", + "Version": "1.8-12", + "Source": "Repository", + "Date": "2023-04-11", + "Title": "S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)", + "Authors@R": "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\", comment = c(ORCID = \"0000-0003-0918-3766\")), person(given = \"Gabor\", family = \"Grothendieck\", role = \"aut\", email = \"ggrothendieck@gmail.com\"), person(given = c(\"Jeffrey\", \"A.\"), family = \"Ryan\", role = \"aut\", email = \"jeff.a.ryan@gmail.com\"), person(given = c(\"Joshua\", \"M.\"), family = \"Ulrich\", role = \"ctb\", email = \"josh.m.ulrich@gmail.com\"), person(given = \"Felix\", family = \"Andrews\", role = \"ctb\", email = \"felix@nfrac.org\"))", + "Description": "An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.", + "Depends": [ + "R (>= 3.1.0)", + "stats" + ], + "Suggests": [ + "AER", + "coda", + "chron", + "ggplot2 (>= 3.0.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tis", + "tseries", + "xts" + ], + "Imports": [ + "utils", + "graphics", + "grDevices", + "lattice (>= 0.20-27)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://zoo.R-Forge.R-project.org/", + "NeedsCompilation": "yes", + "Author": "Achim Zeileis [aut, cre] (), Gabor Grothendieck [aut], Jeffrey A. Ryan [aut], Joshua M. Ulrich [ctb], Felix Andrews [ctb]", + "Maintainer": "Achim Zeileis ", + "Repository": "RSPM", + "Encoding": "UTF-8" + } + } +} diff --git a/renv/.gitignore b/renv/.gitignore new file mode 100644 index 00000000..0ec0cbba --- /dev/null +++ b/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/renv/activate.R b/renv/activate.R new file mode 100644 index 00000000..2c9127fa --- /dev/null +++ b/renv/activate.R @@ -0,0 +1,1304 @@ +local({ + + # the requested version of renv + version <- "1.0.11" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + ansify <- function(text) { + if (renv_ansify_enabled()) + renv_ansify_enhanced(text) + else + renv_ansify_default(text) + } + + renv_ansify_enabled <- function() { + + override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA) + if (!is.na(override)) + return(as.logical(override)) + + pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA) + if (identical(pane, "build")) + return(FALSE) + + testthat <- Sys.getenv("TESTTHAT", unset = "false") + if (tolower(testthat) %in% "true") + return(FALSE) + + iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false") + if (tolower(iderun) %in% "false") + return(FALSE) + + TRUE + + } + + renv_ansify_default <- function(text) { + text + } + + renv_ansify_enhanced <- function(text) { + + # R help links + pattern <- "`\\?(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # return ansified text + text + + } + + renv_ansify_init <- function() { + + envir <- renv_envir_self() + if (renv_ansify_enabled()) + assign("ansify", renv_ansify_enhanced, envir = envir) + else + assign("ansify", renv_ansify_default, envir = envir) + + } + + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + text <- paste(substring(lines, common), collapse = "\n") + + # substitute in ANSI links for executable renv code + ansify(text) + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(url) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + + # retrieve package database + db <- tryCatch( + as.data.frame( + do.call(utils::available.packages, args), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_github_token <- function() { + for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(envval) + } + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + token <- renv_bootstrap_github_token() + if (nzchar(Sys.which("curl")) && nzchar(token)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, token) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 00000000..ffdbb320 --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": null, + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/resources/rmarkdown/chunk07.png b/resources/rmarkdown/chunk07.png index f152943b..e6c063d1 100644 Binary files a/resources/rmarkdown/chunk07.png and b/resources/rmarkdown/chunk07.png differ