diff --git a/.Rprofile b/.Rprofile.bak similarity index 100% rename from .Rprofile rename to .Rprofile.bak diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index e7bad16..c28a589 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -26,6 +26,10 @@ jobs: - {os: macOS-latest, r: 'release'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-24.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"} + - {os: ubuntu-24.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true @@ -33,13 +37,13 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - name: Query dependencies run: | @@ -50,7 +54,7 @@ jobs: - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v2 + uses: actions/cache@v4 with: path: ${{ env.R_LIBS_USER }} key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} @@ -78,7 +82,7 @@ jobs: - name: Upload check results if: failure() - uses: actions/upload-artifact@main + uses: actions/upload-artifact@v4 with: name: ${{ runner.os }}-r${{ matrix.config.r }}-results path: check diff --git a/DESCRIPTION b/DESCRIPTION index 0e87644..72429e5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,9 +7,8 @@ Authors@R: role = c("aut", "cre"), email = "packages@jaredlander.com", comment = c(ORCID = "0000-0002-7291-726X")) -Version: 1.2.8 -Date: 2022-01-12 -Maintainer: Jared P. Lander +Version: 1.2.9 +Date: 2025-08-23 Description: Plots the coefficients from model objects. This very quickly shows the user the point estimates and confidence intervals for fitted models. License: BSD_3_clause + file LICENSE LazyLoad: yes @@ -27,7 +26,7 @@ Imports: purrr, plotly ByteCompile: TRUE -Packaged: 2018-01-02 Jared +Packaged: 2025-08-23 Jared Suggests: testthat (>= 2.0.0), covr, @@ -39,4 +38,4 @@ Suggests: knitr, rmarkdown Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.3.2 diff --git a/NAMESPACE b/NAMESPACE index 23a8daf..02194c6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -7,11 +7,20 @@ S3method(coefplot,data.frame) S3method(coefplot,default) S3method(coefplot,glm) S3method(coefplot,lm) +S3method(coefplot,model_fit) S3method(coefplot,rxGlm) S3method(coefplot,rxLinMod) S3method(coefplot,rxLogit) +S3method(coefplot,workflow) S3method(extract.coef,cv.glmnet) +S3method(extract.coef,default) +S3method(extract.coef,glm) +S3method(extract.coef,glmnet) +S3method(extract.coef,lm) S3method(extract.coef,maxLik) +S3method(extract.coef,rxGlm) +S3method(extract.coef,rxLinMod) +S3method(extract.coef,rxLogit) S3method(extract.coef,xgb.Booster) S3method(extractPath,cv.glmnet) S3method(extractPath,glmnet) diff --git a/R/buildPlot.r b/R/buildPlot.r index aa3f61a..8ceb1c0 100644 --- a/R/buildPlot.r +++ b/R/buildPlot.r @@ -82,13 +82,13 @@ buildPlotting.default <- function( ## build the layer infos outerCIGeom <- geom_errorbarh( - aes_string(xmin="LowOuter", xmax="HighOuter", color="Model", linetype="Model"), + aes(xmin=.data[["LowOuter"]], xmax=.data[["HighOuter"]], color=.data[["Model"]], linetype=.data[["Model"]]), lwd=lwdOuter, height=errorHeight, position=position_dodgev(height=dodgeHeight), na.rm=TRUE ) innerCIGeom <- geom_errorbarh( - aes_string(xmin="LowInner", xmax="HighInner", color="Model", linetype="Model"), + aes(xmin=.data[["LowInner"]], xmax=.data[["HighInner"]], color=.data[["Model"]], linetype=.data[["Model"]]), lwd=lwdInner, height=errorHeight, position=position_dodgev(height=dodgeHeight), na.rm=TRUE ) @@ -97,7 +97,7 @@ buildPlotting.default <- function( #ribbonGeom <- list(None=NULL, geom_ribbon(aes(ymin=LowOuter, ymax=HighOuter, group=Checkers), data=modelCI, fill=fillColor, alpha=alpha, lwd=lwdOuter)) # point layer - pointGeom <- geom_point(aes_string(x=value, color="Model", shape="Model"), size=pointSize, position=position_dodgev(height=dodgeHeight)) + pointGeom <- geom_point(aes(x=.data[[value]], color=.data[["Model"]], shape=.data[["Model"]]), size=pointSize, position=position_dodgev(height=dodgeHeight)) #colorAes <- list(None=NULL, Single=aes(color=as.factor(Model))) colorScaleSingle <- scale_color_manual(values=rep(color, length(unique(modelCI$Model))), guide='none') @@ -110,8 +110,8 @@ buildPlotting.default <- function( faceting <- list(None=NULL, Display=facet_wrap(~Checkers, scales=scales)) # for a regular coefplot or a multiplot in seperate facets - #p <- ggplot(data=modelCI, aes_string(x=value)) - p <- ggplot(data=modelCI, aes_string(x=value, y=coefficient)) # the basics of the plot + #p <- ggplot(data=modelCI, aes(x=.data[[value]])) + p <- ggplot(data=modelCI, aes(x=.data[[value]], y=.data[[coefficient]])) # the basics of the plot #p <- p + colorAes[[1 + multi]] # # in case model needs to be factorized, do it here p <- p + geom_vline(xintercept=0, colour=zeroColor, linetype=zeroType, lwd=zeroLWD) # the zero line p <- p + outerCIGeom + # the outer CI bars diff --git a/R/coefplot-package.r b/R/coefplot-package.r index 0e94b98..d5466b2 100644 --- a/R/coefplot-package.r +++ b/R/coefplot-package.r @@ -1,13 +1,13 @@ +#' @keywords internal +"_PACKAGE" #' Plotting Model Coefficients -#' -#' Provides an S3 generic method for plotting coefficients from a model so it can be extended to other model types. -#' -#' Currently, methods are available for lm, glm and rxLinMod objects. -#' -# @import plyr ggplot2 reshape2 -#' @docType package +#' @description +#' A short description... +#' Provides an S3 generic method for plotting coefficients from a model so it can be extended to other model types. #' @name coefplot -#' @aliases coefplot-package +# @aliases coefplot-package + +# @import plyr ggplot2 reshape2 NULL diff --git a/R/coefplot.r b/R/coefplot.r index 39f29e8..fd78d31 100644 --- a/R/coefplot.r +++ b/R/coefplot.r @@ -99,8 +99,8 @@ coefplot <- function(model, ...) #' @param shorten logical or character; If \code{FALSE} then coefficients for factor levels will include their variable name. If \code{TRUE} coefficients for factor levels will be stripped of their variable names. If a character vector of variables only coefficients for factor levels associated with those variables will the variable names stripped. Currently not available. #' @param interactive If \code{TRUE} an interactive plot is generated instead of \code{ggplot2} #' @param \dots Arguments passed on to other functions -#' @return If \code{plot} is \code{TRUE} then a \code{\link{ggplot}} object is returned. Otherwise a \code{\link{data.frame}} listing coefficients and confidence bands is returned. -#' @seealso \code{\link{lm}} \code{\link{glm}} \code{\link{ggplot}} \code{\link{coefplot}} \code{\link{plotcoef}} +#' @return If \code{plot} is \code{TRUE} then a \code{\link[ggplot2]{ggplot}} object is returned. Otherwise a \code{\link{data.frame}} listing coefficients and confidence bands is returned. +#' @seealso \code{\link{lm}} \code{\link[stats]{glm}} \code{\link[ggplot2]{ggplot}} \code{\link{coefplot}} \code{\link{plotcoef}} #' @export coefplot.default #' @export #' @describeIn coefplot Default method @@ -283,9 +283,9 @@ coefplot.lm <- function(...) #' coefplot.glm #' -# Dotplot for glm coefficients +#' Dotplot for glm coefficients #' -# A graphical display of the coefficients and standard errors from a fitted glm model +#' A graphical display of the coefficients and standard errors from a fitted glm model #' # \code{\link{coefplot}} is the S3 generic method for plotting the coefficients from a fitted model. #' @@ -314,6 +314,7 @@ coefplot.glm <- function(...) #' @title coefplot.workflow #' @description Coefplot method for workflow objects #' @details Pulls model element out of workflow object then calls \code{coefplot}. +#' @export # @author Jared P. Lander #' @describeIn coefplot \code{tidymodels workflows} #' @param model A workflow object @@ -326,6 +327,7 @@ coefplot.workflow <- function(model, ...) #' @title coefplot.model_fit #' @description Coefplot method for parsnip objects #' @details Pulls model element out of parsnip object then calls \code{coefplot}. +#' @export # @author Jared P. Lander #' @describeIn coefplot \code{parsnip} #' @param model A parsnip object diff --git a/R/extractCoef.r b/R/extractCoef.r index 772a216..1f9e361 100644 --- a/R/extractCoef.r +++ b/R/extractCoef.r @@ -7,6 +7,7 @@ #' #' @author Jared P. Lander #' @method extract.coef default +#' @export #' @aliases extract.coef.default #' @param model Model object to extract information from. #' @param \dots Further arguments @@ -45,6 +46,7 @@ extract.coef.default <- function(model, ...) #' @author Jared P. Lander #' @aliases extract.coef.lm #' @method extract.coef lm +#' @export #' @inheritParams extract.coef.default #' @return A \code{\link{data.frame}} containing the coefficient, the standard #' error and the variable name. @@ -73,6 +75,7 @@ extract.coef.lm <- function(model, ...) #' @aliases extract.coef.glm #' @inheritParams extract.coef.default #' @method extract.coef glm +#' @export #' @return A \code{\link{data.frame}} containing the coefficient, the standard #' error and the variable name. #' @examples @@ -136,6 +139,7 @@ extract.coef <- function(model, ...) #' @aliases extract.coef.rxLinMod #' @inheritParams extract.coef.default #' @method extract.coef rxLinMod +#' @export #' @return A \code{\link{data.frame}} containing the coefficient, the standard #' error and the variable name. #' @examples @@ -172,6 +176,7 @@ extract.coef.rxLinMod <- function(model, ...) #' @aliases extract.coef.rxGlm #' @inheritParams extract.coef.default #' @method extract.coef rxGlm +#' @export #' @return A \code{\link{data.frame}} containing the coefficient, the standard #' error and the variable name. #' @examples @@ -201,6 +206,7 @@ extract.coef.rxGlm <- function(model, ...) #' @aliases extract.coef.rxLogit #' @inheritParams extract.coef.default #' @method extract.coef rxLogit +#' @export #' @return A \code{\link{data.frame}} containing the coefficient, the standard #' error and the variable name. #' @examples @@ -216,12 +222,30 @@ extract.coef.rxLogit <- function(model, ...) extract.coef.default(model=model, ...) } +# #' @title extract.coef.glmnet +# #' @description Extract Coefficient Information from Models +# #' @details Gets the coefficient values and variable names from a model. Since +# #' glmnet does not have standard errors, those will just be NA. +# #' @author Jared P. Lander +# #' @method extract.coef glmnet +# #' @aliases extract.coef.elnet +# #' @param model Model object from which to extract information. +# #' @param lambda Value of penalty parameter +# #' @param \dots Further arguments +# #' @return A \code{\link{data.frame}} containing the coefficient, the standard +# #' error and the variable name. +# extract.coef.elnet <- function(model, lambda=stats::median(model$lambda), ...) +# { +# extract.coef.glmnet(model, lambda, ...) +# } + #' @title extract.coef.glmnet #' @description Extract Coefficient Information from Models #' @details Gets the coefficient values and variable names from a model. Since #' glmnet does not have standard errors, those will just be NA. #' @author Jared P. Lander #' @method extract.coef glmnet +#' @export #' @aliases extract.coef.glmnet #' @param model Model object from which to extract information. #' @param lambda Value of penalty parameter @@ -233,12 +257,12 @@ extract.coef.rxLogit <- function(model, ...) #' library(glmnet) #' library(ggplot2) #' library(useful) +#' library(coefplot) #' data(diamonds) #' diaX <- build.x(price ~ carat + cut + x - 1, data=diamonds, contrasts = TRUE) #' diaY <- build.y(price ~ carat + cut + x - 1, data=diamonds) #' modG1 <- glmnet(x=diaX, y=diaY) #' extract.coef(modG1) -#' } #' \dontshow{\}} #' extract.coef.glmnet <- function(model, lambda=stats::median(model$lambda), ...) @@ -317,7 +341,6 @@ extract.coef.cv.glmnet <- function(model, lambda="lambda.min", ...) #' N <- length(x) #' res <- maxLik(loglik, start=c(0,1)) # use 'wrong' start values #' extract.coef(res) -#' } #' \dontshow{ #' \} #' } diff --git a/R/position.r b/R/position.r index 2ec1a54..54e0d39 100644 --- a/R/position.r +++ b/R/position.r @@ -112,7 +112,6 @@ pos_dodgev <- function(df, height) { #' Adjust position by dodging overlaps to the side. #' -#' @inheritParams ggplot2::position_identity #' @param height Dodging height, when different to the height of the individual #' elements. This is useful when you want to align narrow geoms with wider #' geoms. See the examples for a use case. diff --git a/cran-comments.md b/cran-comments.md index 1d1095b..6687f3b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,6 @@ ## Version Number -1.2.8 +1.2.9 ## Test environments @@ -9,20 +9,15 @@ - macOS-latest (release) - ubuntu-20.04 (release) - ubuntu-20.04 (devel) -- Windows 10, R 4.1.0 -- Ubuntu 18.04, R 4.1.2 -- Win-Builder -- R-Hub + - ubuntu-22.04 (release) + - ubuntu-22.04 (devel) + - ubuntu-24.04 (release) + - ubuntu-24.04 (devel) +- Ubuntu 12.04, R 4.5.1 ## R CMD check results -There were no ERRORs, WARNINGs, NOTEs when checked locally on Windows and Ubuntu or the GitHub Actions for Windows or Ubuntu-release. - -GitHub Actions for Mac and Ubuntu-devel had a notes of an example taking more than 5 seconds, though I imagine that has more to do with the machine doing the testing. - -WinBuild had a note of an example taking more than 10 seconds, though I imagine that has more to do with the machine doing the testing. - -R-Hub had a note of an example taking more than 5 seconds, though I imagine that has more to do with the machine doing the testing. +There were no ERRORs, WARNINGs, NOTEs when checked locally on Ubuntu or the GitHub Actions for Windows or Mac. For Github Actions with Ubuntu-release there were no ERRORs or WARNINGs, just a NOTE, but that was related to the executiobn time of examples, likely due to using slow runners. ## Tests diff --git a/man/coefplot-package.Rd b/man/coefplot-package.Rd new file mode 100644 index 0000000..13a6a58 --- /dev/null +++ b/man/coefplot-package.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/coefplot-package.r +\docType{package} +\name{coefplot-package} +\alias{coefplot-package} +\title{coefplot: Plots Coefficients from Fitted Models} +\description{ +Plots the coefficients from model objects. This very quickly shows the user the point estimates and confidence intervals for fitted models. +} +\author{ +\strong{Maintainer}: Jared Lander \email{packages@jaredlander.com} (\href{https://orcid.org/0000-0002-7291-726X}{ORCID}) + +} +\keyword{internal} diff --git a/man/coefplot.Rd b/man/coefplot.Rd index 52cba73..70a3588 100644 --- a/man/coefplot.Rd +++ b/man/coefplot.Rd @@ -1,9 +1,7 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/coefplot-package.r, R/coefplot.r -\docType{package} \name{coefplot} \alias{coefplot} -\alias{coefplot-package} \alias{plotcoef} \alias{coefplot.default} \alias{coefplot.lm} @@ -152,7 +150,7 @@ coefplot(model, ...) \value{ A ggplot2 object or data.frame. See details in \code{\link{coefplot.lm}} for more information -If \code{plot} is \code{TRUE} then a \code{\link{ggplot}} object is returned. Otherwise a \code{\link{data.frame}} listing coefficients and confidence bands is returned. +If \code{plot} is \code{TRUE} then a \code{\link[ggplot2]{ggplot}} object is returned. Otherwise a \code{\link{data.frame}} listing coefficients and confidence bands is returned. A ggplot object. See \code{\link{coefplot.lm}} for more information. @@ -161,7 +159,8 @@ A ggplot object. See \code{\link{coefplot.lm}} for more information. A ggplot object. See \code{\link{coefplot.lm}} for more information. } \description{ -Provides an S3 generic method for plotting coefficients from a model so it can be extended to other model types. +A short description... + Provides an S3 generic method for plotting coefficients from a model so it can be extended to other model types. A graphical display of the coefficients and standard errors from a fitted model @@ -169,12 +168,16 @@ A graphical display of the coefficients and standard errors from a fitted model This can be extended with new methods for other types of models not currently available. +Dotplot for glm coefficients + Coefplot method for workflow objects Coefplot method for parsnip objects } \details{ -Currently, methods are available for lm, glm and rxLinMod objects. +A graphical display of the coefficients and standard errors from a fitted glm model + + For more information on this function and it's arguments see \code{\link{coefplot.default}} @@ -184,23 +187,23 @@ Pulls model element out of parsnip object then calls \code{coefplot}. } \section{Methods (by class)}{ \itemize{ -\item \code{default}: Default method +\item \code{coefplot(default)}: Default method -\item \code{lm}: \code{lm} +\item \code{coefplot(lm)}: \code{lm} -\item \code{glm}: \code{glm} +\item \code{coefplot(glm)}: \code{glm} -\item \code{workflow}: \code{tidymodels workflows} +\item \code{coefplot(workflow)}: \code{tidymodels workflows} -\item \code{model_fit}: \code{parsnip} +\item \code{coefplot(model_fit)}: \code{parsnip} -\item \code{rxGlm}: \code{rxGlm} +\item \code{coefplot(rxGlm)}: \code{rxGlm} -\item \code{rxLinMod}: \code{rxLinMod} +\item \code{coefplot(rxLinMod)}: \code{rxLinMod} -\item \code{rxLogit}: \code{rxLogit} -}} +\item \code{coefplot(rxLogit)}: \code{rxLogit} +}} \examples{ data(diamonds) @@ -264,7 +267,7 @@ coefplot(mod6) \seealso{ \code{\link{coefplot.lm}} \code{\link{coefplot.data.frame}} -\code{\link{lm}} \code{\link{glm}} \code{\link{ggplot}} \code{\link{coefplot}} \code{\link{plotcoef}} +\code{\link{lm}} \code{\link[stats]{glm}} \code{\link[ggplot2]{ggplot}} \code{\link{coefplot}} \code{\link{plotcoef}} } \author{ Jared P. Lander diff --git a/man/extract.coef.glmnet.Rd b/man/extract.coef.glmnet.Rd index 9037b53..3e59a27 100644 --- a/man/extract.coef.glmnet.Rd +++ b/man/extract.coef.glmnet.Rd @@ -23,6 +23,20 @@ Extract Coefficient Information from Models \details{ Gets the coefficient values and variable names from a model. Since glmnet does not have standard errors, those will just be NA. +} +\examples{ +\dontshow{if(requireNamespace('glmnet', quietly=TRUE))\{} +library(glmnet) +library(ggplot2) +library(useful) +library(coefplot) +data(diamonds) +diaX <- build.x(price ~ carat + cut + x - 1, data=diamonds, contrasts = TRUE) +diaY <- build.y(price ~ carat + cut + x - 1, data=diamonds) +modG1 <- glmnet(x=diaX, y=diaY) +extract.coef(modG1) +\dontshow{\}} + } \author{ Jared P. Lander diff --git a/man/extract.coef.maxLik.Rd b/man/extract.coef.maxLik.Rd index 2f739bf..9d0b490 100644 --- a/man/extract.coef.maxLik.Rd +++ b/man/extract.coef.maxLik.Rd @@ -20,6 +20,27 @@ Extract Coefficient Information from Models } \details{ Gets the coefficient values and variable names from a model. +} +\examples{ +\dontshow{ +if(requireNamespace('maxLik', quietly=TRUE)) +\{ +} +library(maxLik) +loglik <- function(param) { + mu <- param[1] + sigma <- param[2] + ll <- -0.5*N*log(2*pi) - N*log(sigma) - sum(0.5*(x - mu)^2/sigma^2) +ll +} +x <- rnorm(1000, 1, 2) # use mean=1, stdd=2 +N <- length(x) +res <- maxLik(loglik, start=c(0,1)) # use 'wrong' start values +extract.coef(res) +\dontshow{ +\} +} + } \author{ Jared P. Lander diff --git a/renv.lock b/renv.lock index 71f95c9..5b3e5af 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.1.2", + "Version": "4.5.1", "Repositories": [ { "Name": "CRAN", @@ -11,857 +11,5323 @@ "Packages": { "KernSmooth": { "Package": "KernSmooth", - "Version": "2.23-20", + "Version": "2.23-26", "Source": "Repository", - "Repository": "CRAN", - "Hash": "8dcfa99b14c296bc9f1fd64d52fd3ce7" + "Priority": "recommended", + "Date": "2024-12-10", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"Brian.Ripley@R-project.org\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", + "stats" + ], + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".", + "License": "Unlimited", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MASS": { "Package": "MASS", - "Version": "7.3-54", + "Version": "7.3-65", "Source": "Repository", - "Repository": "CRAN", - "Hash": "0e59129db205112e3963904db67fd0dc" + "Priority": "recommended", + "Date": "2025-02-19", + "Revision": "$Rev: 3681 $", + "Depends": [ + "R (>= 4.4.0)", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"Brian.Ripley@R-project.org\"), person(\"Bill\", \"Venables\", role = c(\"aut\", \"cph\")), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\", comment = \"support functions for polr\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [aut, cph], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb] (support functions for polr)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "Matrix": { "Package": "Matrix", - "Version": "1.3-4", + "Version": "1.7-3", "Source": "Repository", - "Repository": "CRAN", - "Hash": "4ed05e9c9726267e4a5872e09c04587c" + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2025-03-05", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.73): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (ORCID: ), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "data.table": { "Package": "data.table", - "Version": "1.14.2", + "Version": "1.17.8", "Source": "Repository", - "Repository": "RSPM", - "Hash": "36b67b5adf57b292923f5659f5f0c853" + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "methods" + ], + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Ivan\", 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[aut] (ORCID: ), Toby Hocking [aut] (ORCID: ), Benjamin Schwendinger [aut] (ORCID: ), Ivan Krylov [aut] (ORCID: ), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan 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"1.4.3", "Source": "Repository", - "Repository": "RSPM", - "Hash": "28763d08fadd0b733e3cee9dab4e12fe" + "Title": "Manipulate DESCRIPTION Files", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", role = \"aut\"), person(\"Jim\", \"Hester\", , \"james.f.hester@gmail.com\", role = \"aut\"), person(\"Maëlle\", \"Salmon\", role = \"ctb\", comment = c(ORCID = \"0000-0002-2815-0399\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Maintainer": "Gábor Csárdi ", + "Description": "Tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.", + "License": "MIT + file LICENSE", + "URL": "https://desc.r-lib.org/, https://github.com/r-lib/desc", + "BugReports": "https://github.com/r-lib/desc/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli", + "R6", + "utils" + ], + "Suggests": [ + "callr", + "covr", + "gh", + "spelling", + "testthat", + "whoami", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "Collate": "'assertions.R' 'authors-at-r.R' 'built.R' 'classes.R' 'collate.R' 'constants.R' 'deps.R' 'desc-package.R' 'description.R' 'encoding.R' 'find-package-root.R' 'latex.R' 'non-oo-api.R' 'package-archives.R' 'read.R' 'remotes.R' 'str.R' 'syntax_checks.R' 'urls.R' 'utils.R' 'validate.R' 'version.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Kirill Müller [aut], Jim Hester [aut], Maëlle Salmon [ctb] (), Posit Software, PBC [cph, fnd]", + "Repository": "CRAN" + }, + "diagram": { + "Package": "diagram", + "Version": "1.6.5", + "Source": "Repository", + "Title": "Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams", + "Author": "Karline Soetaert ", + "Maintainer": "Karline Soetaert ", + "Depends": [ + "R (>= 2.01)", + "shape" + ], + "Imports": [ + "stats", + "graphics" + ], + "Description": "Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book \"A practical guide to ecological modelling - using R as a simulation platform\" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb).", + "License": "GPL (>= 2)", + "LazyData": "yes", + "NeedsCompilation": "no", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest", + "Encoding": "UTF-8" }, "diffobj": { "Package": "diffobj", - "Version": "0.3.5", + "Version": "0.3.6", "Source": "Repository", - "Repository": "RSPM", - "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" + "Type": "Package", + "Title": "Diffs for R Objects", + "Description": "Generate a colorized diff of two R objects for an intuitive visualization of their differences.", + "Authors@R": "c( person( \"Brodie\", \"Gaslam\", email=\"brodie.gaslam@yahoo.com\", role=c(\"aut\", \"cre\")), person( \"Michael B.\", \"Allen\", email=\"ioplex@gmail.com\", role=c(\"ctb\", \"cph\"), comment=\"Original C implementation of Myers Diff Algorithm\"))", + "Depends": [ + "R (>= 3.1.0)" + ], + "License": "GPL-2 | GPL-3", + "URL": "https://github.com/brodieG/diffobj", + "BugReports": "https://github.com/brodieG/diffobj/issues", + "RoxygenNote": "7.2.3", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "Suggests": [ + "knitr", + "rmarkdown" + ], + "Collate": "'capt.R' 'options.R' 'pager.R' 'check.R' 'finalizer.R' 'misc.R' 'html.R' 'styles.R' 's4.R' 'core.R' 'diff.R' 'get.R' 'guides.R' 'hunks.R' 'layout.R' 'myerssimple.R' 'rdiff.R' 'rds.R' 'set.R' 'subset.R' 'summmary.R' 'system.R' 'text.R' 'tochar.R' 'trim.R' 'word.R'", + "Imports": [ + "crayon (>= 1.3.2)", + "tools", + "methods", + "utils", + "stats" + ], + "NeedsCompilation": "yes", + "Author": "Brodie Gaslam [aut, cre], Michael B. Allen [ctb, cph] (Original C implementation of Myers Diff Algorithm)", + "Maintainer": "Brodie Gaslam ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "digest": { "Package": "digest", - "Version": "0.6.29", + "Version": "0.6.37", "Source": "Repository", - "Repository": "RSPM", - "Hash": "cf6b206a045a684728c3267ef7596190" + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. 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": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "dplyr": { "Package": "dplyr", - 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Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.", + "License": "MIT + file LICENSE", + "Depends": [ + "R (>= 3.0)" + ], + "Imports": [ + "magrittr", + "htmlwidgets (>= 0.6)", + "htmltools (>= 0.3.5)", + "zoo (>= 1.7-10)", + "xts (>= 0.9-7)" + ], + "Suggests": [ + "testthat" + ], + "Enhances": [ + "rmarkdown (>= 0.3.3)", + "shiny (>= 0.10.2.1)" + ], + "RoxygenNote": "6.0.1", + "NeedsCompilation": "no", + "Author": "Dan Vanderkam [aut, cph] (dygraphs library in htmlwidgets/lib, http://dygraphs.com/), Petr Shevtsov [cre, cph], JJ Allaire [aut], RStudio [cph], Jonathan Owen [aut, cph], Daniel Gromer [aut, cph], Benoit Thieurmel [aut, cph], Kent Laukhuf [ctb], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/htmlwidgets/lib/jquery/AUTHORS.txt)", + "Maintainer": "Petr Shevtsov ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest", + "Encoding": "UTF-8" }, "evaluate": { "Package": "evaluate", - "Version": "0.14", + "Version": "1.0.4", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ec8ca05cffcc70569eaaad8469d2a3a7" - }, - "fansi": { - "Package": "fansi", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "RSPM", - "Hash": "ae34c3d1fdfac1566ca17c1b5d8f2613" + "Type": "Package", + "Title": "Parsing and Evaluation Tools that Provide More Details than the Default", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Yihui\", \"Xie\", role = \"aut\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Michael\", \"Lawrence\", role = \"ctb\"), person(\"Thomas\", \"Kluyver\", role = \"ctb\"), person(\"Jeroen\", \"Ooms\", role = \"ctb\"), person(\"Barret\", \"Schloerke\", role = \"ctb\"), person(\"Adam\", \"Ryczkowski\", role = \"ctb\"), person(\"Hiroaki\", \"Yutani\", role = \"ctb\"), person(\"Michel\", \"Lang\", role = \"ctb\"), person(\"Karolis\", \"Koncevičius\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.", + "License": "MIT + file LICENSE", + "URL": "https://evaluate.r-lib.org/, https://github.com/r-lib/evaluate", + "BugReports": "https://github.com/r-lib/evaluate/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Suggests": [ + "callr", + "covr", + "ggplot2 (>= 3.3.6)", + "lattice", + "methods", + "pkgload", + "ragg (>= 1.4.0)", + "rlang (>= 1.1.5)", + "knitr", + "testthat (>= 3.0.0)", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut, cre], Yihui Xie [aut] (ORCID: ), Michael Lawrence [ctb], Thomas Kluyver [ctb], Jeroen Ooms [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb], Hiroaki Yutani [ctb], Michel Lang [ctb], Karolis Koncevičius [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "farver": { "Package": "farver", - "Version": "2.1.0", + "Version": "2.1.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "c98eb5133d9cb9e1622b8691487f11bb" + "Type": "Package", + "Title": "High Performance Colour Space Manipulation", + "Authors@R": "c( person(\"Thomas Lin\", \"Pedersen\", , \"thomas.pedersen@posit.co\", role = c(\"cre\", \"aut\"), comment = c(ORCID = \"0000-0002-5147-4711\")), person(\"Berendea\", \"Nicolae\", role = \"aut\", comment = \"Author of the ColorSpace C++ library\"), person(\"Romain\", \"François\", , \"romain@purrple.cat\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Posit, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The encoding of colour can be handled in many different ways, using different colour spaces. 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The 'farver' package provides a set of functions that gives access to very fast colour space conversion and comparisons implemented in C++, and offers speed improvements over the 'convertColor' function in the 'grDevices' package.", + "License": "MIT + file LICENSE", + "URL": "https://farver.data-imaginist.com, https://github.com/thomasp85/farver", + "BugReports": "https://github.com/thomasp85/farver/issues", + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Thomas Lin Pedersen [cre, aut] (), Berendea Nicolae [aut] (Author of the ColorSpace C++ library), Romain François [aut] (), Posit, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "fastmap": { "Package": "fastmap", - "Version": "1.1.0", + "Version": "1.2.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "77bd60a6157420d4ffa93b27cf6a58b8" + "Title": "Fast Data Structures", + "Authors@R": "c( person(\"Winston\", \"Chang\", email = \"winston@posit.co\", role = c(\"aut\", \"cre\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(given = \"Tessil\", role = \"cph\", comment = \"hopscotch_map library\") )", + "Description": "Fast implementation of data structures, including a key-value store, stack, and queue. 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With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.", + "Depends": [ + "R (>= 3.4.0)" + ], + "Imports": [ + "ggplot2", + "graphics", + "grDevices", + "grid", + "gridGraphics", + "yulab.utils" + ], + "Suggests": [ + "aplot", + "colorspace", + "cowplot", + "ggimage", + "knitr", + "rmarkdown", + "lattice", + "prettydoc", + "vcd", + "utils" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "License": "Artistic-2.0", + "URL": "https://github.com/GuangchuangYu/ggplotify", + "BugReports": "https://github.com/GuangchuangYu/ggplotify/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Guangchuang Yu [aut, cre] ()", + "Maintainer": "Guangchuang Yu ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "glmnet": { "Package": "glmnet", - "Version": "4.1-3", + "Version": "4.1-10", "Source": "Repository", - "Repository": "CRAN", - "Hash": "c2212436f9c51ebb6a4df7ba616662c1" + "Type": "Package", + "Title": "Lasso and Elastic-Net Regularized Generalized Linear Models", + "Date": "2025-07-15", + "Authors@R": "c(person(\"Jerome\", \"Friedman\", role=c(\"aut\")), person(\"Trevor\", \"Hastie\", role=c(\"aut\", \"cre\"), email = \"hastie@stanford.edu\"), person(\"Rob\", \"Tibshirani\", role=c(\"aut\")), person(\"Balasubramanian\", \"Narasimhan\", role=c(\"aut\")), person(\"Kenneth\",\"Tay\",role=c(\"aut\")), person(\"Noah\", \"Simon\", role=c(\"aut\")), person(\"Junyang\", \"Qian\", role=c(\"ctb\")), person(\"James\", \"Yang\", role=c(\"aut\")))", + "Depends": [ + "R (>= 3.6.0)", + "Matrix (>= 1.0-6)" + ], + "Imports": [ + "methods", + "utils", + "foreach", + "shape", + "survival", + "Rcpp" + ], + "Suggests": [ + "knitr", + "lars", + "testthat", + "xfun", + "rmarkdown" + ], + "SystemRequirements": "C++17", + "Description": "Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression, Cox model, multiple-response Gaussian, and the grouped multinomial regression; see and . There are two new and important additions. The family argument can be a GLM family object, which opens the door to any programmed family (). This comes with a modest computational cost, so when the built-in families suffice, they should be used instead. The other novelty is the relax option, which refits each of the active sets in the path unpenalized. 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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 (>= 4.0)" + ], + "Imports": [ + "cli", + "glue", + "grid", + "lifecycle", + "rlang (>= 1.1.0)", + "stats" + ], + "Suggests": [ + "covr", + "ggplot2", + "knitr", + "profvis", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/usethis/last-upkeep": "2024-10-25", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Hadley Wickham [aut], Thomas Lin Pedersen [aut, cre], Posit Software, PBC [cph, fnd]", + "Maintainer": "Thomas Lin Pedersen ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "hardhat": { "Package": "hardhat", - "Version": "0.1.6", + "Version": "1.4.2", "Source": "Repository", - "Repository": "RSPM", - "Hash": "0a6d19a347ba196bec25e71bec548083" + "Title": "Construct Modeling Packages", + "Authors@R": "c( person(\"Hannah\", \"Frick\", , \"hannah@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6049-5258\")), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = \"aut\"), person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "Building modeling packages is hard. 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To quote Rene Magritte, \"Ceci n'est pas un pipe.\"", + "License": "MIT + file LICENSE", + "URL": "https://magrittr.tidyverse.org, https://github.com/tidyverse/magrittr", + "BugReports": "https://github.com/tidyverse/magrittr/issues", + "Depends": [ + "R (>= 3.4.0)" + ], + "Suggests": [ + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "Yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.1.2", + "NeedsCompilation": "yes", + "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], RStudio [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "maxLik": { "Package": "maxLik", - "Version": "1.5-2", + "Version": "1.5-2.1", "Source": "Repository", + "Title": "Maximum Likelihood Estimation and Related Tools", + "Authors@R": "c(person(\"Ott\", \"Toomet\", role=c(\"aut\", \"cre\"), email=\"otoomet@gmail.com\"), person(\"Arne\", \"Henningsen\", role=c(\"aut\"), email=\"arne.henningsen@gmail.com\"), person(\"Spencer\", \"Graves\", role=c(\"ctb\")), person(\"Yves\", \"Croissant\", role=c(\"ctb\")), person(\"David\", \"Hugh-Jones\", role=c(\"ctb\")), person(\"Luca\", \"Scrucca\", role=c(\"ctb\")) )", + "Depends": [ + "R (>= 2.4.0)", + "miscTools (>= 0.6-8)", + "methods" + ], + "Imports": [ + "sandwich", + "generics" + ], + "Suggests": [ + "MASS", + "clue", + "dlm", + "plot3D", + "tibble", + "tinytest" + ], + "Description": "Functions for Maximum Likelihood (ML) estimation, non-linear optimization, and related tools. 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Many of them facilitate the work with matrices, e.g. inserting rows or columns, creating symmetric matrices, or checking for semidefiniteness. Other tools facilitate the work with regression models, e.g. extracting the standard errors, obtaining the number of (estimated) parameters, or calculating R-squared values.", + "License": "GPL (>= 2)", + "URL": "https://github.com/arne-henningsen/miscTools", + "BugReports": "https://github.com/arne-henningsen/miscTools/issues", + "NeedsCompilation": "no", "Repository": "CRAN", - "Hash": "340f0789cb2dcc816d9856d375c1df83" + "Encoding": "UTF-8" }, - "munsell": { - "Package": "munsell", - "Version": "0.5.0", + "modelenv": { + "Package": "modelenv", + "Version": "0.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "6dfe8bf774944bd5595785e3229d8771" + "Title": "Provide Tools to Register Models for Use in 'tidymodels'", + "Authors@R": "c( person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0679-1945\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "An developer focused, low dependency package in 'tidymodels' that provides functions to register how models are to be used. 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It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.", + "License": "MIT + file LICENSE", + "URL": "https://readr.tidyverse.org, https://github.com/tidyverse/readr", + "BugReports": "https://github.com/tidyverse/readr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.2.0)", + "clipr", + "crayon", + "hms (>= 0.4.1)", + "lifecycle (>= 0.2.0)", + "methods", + "R6", + "rlang", + "tibble", + "utils", + "vroom (>= 1.6.0)" + ], + "Suggests": [ + "covr", + "curl", + "datasets", + "knitr", + "rmarkdown", + "spelling", + "stringi", + "testthat (>= 3.2.0)", + "tzdb (>= 0.1.1)", + "waldo", + "withr", + "xml2" + ], + "LinkingTo": [ + "cpp11", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Jim Hester [aut], Romain Francois [ctb], Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], Posit Software, PBC [cph, fnd], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)", + "Maintainer": "Jennifer Bryan ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, - "renv": { - "Package": "renv", - "Version": "0.13.2", + "recipes": { + "Package": "recipes", + "Version": "1.3.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "079cb1f03ff972b30401ed05623cbe92" + "Title": "Preprocessing and Feature Engineering Steps for Modeling", + "Authors@R": "c( person(\"Max\", \"Kuhn\", , \"max@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Emil\", \"Hvitfeldt\", , \"emil.hvitfeldt@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\"), comment = c(ROR = \"03wc8by49\")) )", + "Description": "A recipe prepares your data for modeling. We provide an extensible framework for pipeable sequences of feature engineering steps provides preprocessing tools to be applied to data. Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. 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Beyond these standards it provides the \"Financial Center\" concept which allows to handle data records collected in different time zones and mix them up to have always the proper time stamps with respect to your personal financial center, or alternatively to the GMT reference time. 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See for more details.", + "Depends": [ + "R (>= 3.3)" + ], + "License": "GPL (>= 3)", + "Encoding": "UTF-8", + "LinkingTo": [ + "cpp11 (>= 0.2.7)" + ], + "Suggests": [ + "testthat (>= 0.7.1.99)", + "knitr" + ], + "SystemRequirements": "A system with zoneinfo data (e.g. /usr/share/zoneinfo) as well as a recent-enough C++11 compiler (such as g++-4.8 or later). On Windows the zoneinfo included with R is used.", + "BugReports": "https://github.com/vspinu/timechange/issues", + "URL": "https://github.com/vspinu/timechange/", + "RoxygenNote": "7.2.1", + "NeedsCompilation": "yes", + "Author": "Vitalie Spinu [aut, cre], Google Inc. [ctb, cph]", + "Maintainer": "Vitalie Spinu ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "tinytex": { "Package": "tinytex", - "Version": "0.36", + "Version": "0.57", "Source": "Repository", - "Repository": "RSPM", - "Hash": "130fe4c61e55b271a2655b3a284a205f" + "Type": "Package", + "Title": "Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4474-2498\")), person(\"Devon\", \"Ryan\", role = \"ctb\", email = \"dpryan79@gmail.com\", comment = c(ORCID = \"0000-0002-8549-0971\")), person(\"Ethan\", \"Heinzen\", role = \"ctb\"), person(\"Fernando\", \"Cagua\", role = \"ctb\"), person() )", + "Description": "Helper functions to install and maintain the 'LaTeX' distribution named 'TinyTeX' (), a lightweight, cross-platform, portable, and easy-to-maintain version of 'TeX Live'. This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" + }, + "tzdb": { + "Package": "tzdb", + "Version": "0.5.0", + "Source": "Repository", + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.5.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "useful": { "Package": "useful", - "Version": "1.2.6", + "Version": "1.2.6.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "62884cf15898e6b7488cb08f1013fd50" + "Type": "Package", + "Title": "A Collection of Handy, Useful Functions", + "Date": "2018-10-07", + "Authors@R": "c( person(c(\"Jared\", \"P.\"), \"Lander\", email = \"packages@jaredlander.com\", role = c(\"cre\", \"aut\")), person(\"Nicholas\", \"Galasinao\", email = \"nicholas.galasinao@gmail.com\", role = \"ctb\"), person(\"Joshua\", \"Kraut\", email = \"joshua.kraut@gmail.com\", role = \"ctb\"), person(\"Daniel\", \"Chen\", email = \"dan dcheny@gmail.com\", role = \"ctb\"))", + "Description": "A set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing parts of a data.frame, constructing formulas from text and building design and response matrices.", + "License": "BSD_3_clause + file LICENSE", + "Depends": [ + "ggplot2" + ], + "Imports": [ + "plyr", + "dplyr (>= 0.5.0)", + "magrittr", + "purrr (>= 0.1.0)", + "stats", + "scales", + "utils", + "Matrix", + "assertthat" + ], + "LazyLoad": "yes", + "ByteCompile": "TRUE", + "Suggests": [ + "testthat", + "tibble", + "covr" + ], + "URL": "https://github.com/jaredlander/useful", + "BugReports": "https://github.com/jaredlander/useful/issues", + "RoxygenNote": "6.1.0", + "NeedsCompilation": "no", + "Author": "Jared P. 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The package is made to be extensible, so that users are also allowed to define their own objectives easily.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://github.com/dmlc/xgboost", + "BugReports": "https://github.com/dmlc/xgboost/issues", + "NeedsCompilation": "yes", + "VignetteBuilder": "knitr", + "Suggests": [ + "knitr", + "rmarkdown", + "ggplot2 (>= 1.0.1)", + "DiagrammeR (>= 0.9.0)", + "Ckmeans.1d.dp (>= 3.3.1)", + "vcd (>= 1.3)", + "cplm", + "e1071", + "caret", + "testthat", + "lintr", + "igraph (>= 1.0.1)", + "float", + "crayon", + "titanic" + ], + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "Matrix (>= 1.1-0)", + "methods", + "data.table (>= 1.9.6)", + "jsonlite (>= 1.0)" + ], + "RoxygenNote": "7.3.2", + "Encoding": "UTF-8", + "SystemRequirements": "GNU make, C++17", + "Author": "Tianqi Chen [aut], Tong He [aut], Michael Benesty [aut], Vadim Khotilovich [aut], Yuan Tang [aut] (ORCID: ), Hyunsu Cho [aut], Kailong Chen [aut], Rory Mitchell [aut], Ignacio Cano [aut], Tianyi Zhou [aut], Mu Li [aut], Junyuan Xie [aut], Min Lin [aut], Yifeng Geng [aut], Yutian Li [aut], Jiaming Yuan [aut, cre], XGBoost contributors [cph] (base XGBoost implementation)", + "Repository": "CRAN" }, "xts": { "Package": "xts", - "Version": "0.12.1", + "Version": "0.14.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "ca2fd4ad8ef78cca3aa2b30f992798a8" + "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": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest" }, "yaml": { "Package": "yaml", - "Version": "2.2.1", + "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": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest", + "Encoding": "UTF-8" + }, + "yulab.utils": { + "Package": "yulab.utils", + "Version": "0.2.1", "Source": "Repository", - "Repository": "RSPM", - "Hash": "2826c5d9efb0a88f657c7a679c7106db" + "Title": "Supporting Functions for Packages Maintained by 'YuLab-SMU'", + "Authors@R": "c(person(\"Guangchuang\", \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6485-8781\")))", + "Description": "Miscellaneous functions commonly used by 'YuLab-SMU'.", + "Depends": [ + "R (>= 4.2.0)" + ], + "Imports": [ + "cli", + "digest", + "fs", + "rappdirs", + "rlang", + "tools", + "utils" + ], + "Suggests": [ + "httr2", + "jsonlite", + "openssl" + ], + "ByteCompile": "true", + "License": "Artistic-2.0", + "URL": "https://yulab-smu.top/", + "BugReports": "https://github.com/YuLab-SMU/yulab.utils/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Guangchuang Yu [aut, cre] (ORCID: )", + "Maintainer": "Guangchuang Yu ", + "Repository": "CRAN" }, "zoo": { "Package": "zoo", - "Version": "1.8-9", + "Version": "1.8-14", "Source": "Repository", - "Repository": "RSPM", - "Hash": "035d1c7c12593038c26fb1c2fd40c4d2" + "Date": "2025-04-09", + "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 (>= 3.5.0)", + "mondate", + "scales", + "stinepack", + "strucchange", + "timeDate", + "timeSeries", + "tinyplot", + "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": "https://rspm.lander.ai/prod-cran/__linux__/jammy/latest", + "Encoding": "UTF-8" } } } diff --git a/renv/.gitignore b/renv/.gitignore index 2129631..6ae4167 100644 --- a/renv/.gitignore +++ b/renv/.gitignore @@ -1,3 +1,5 @@ +cellar/ +sandbox/ library/ local/ lock/ diff --git a/renv/activate.R b/renv/activate.R index b852628..2753ae5 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -2,18 +2,89 @@ local({ # the requested version of renv - version <- "0.13.2" + version <- "1.1.5" + attr(version, "sha") <- NULL # the project directory - project <- getwd() + 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 + # 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 (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA))) + 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 - Sys.setenv("RENV_R_INITIALIZING" = "true") - on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE) + 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) @@ -22,33 +93,155 @@ local({ # mask 'utils' packages, will come first on the search path library(utils, lib.loc = .Library) - # check to see if renv has already been loaded - if ("renv" %in% loadedNamespaces()) { - - # if renv has already been loaded, and it's the requested version of renv, - # nothing to do - spec <- .getNamespaceInfo(.getNamespace("renv"), "spec") - if (identical(spec[["version"]], version)) - return(invisible(TRUE)) - - # otherwise, unload and attempt to load the correct version of renv + # 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;;x-r-help:\\1\a?\\1\033]8;;\a`" + text <- gsub(pattern, replacement, text, perl = TRUE) + + # runnable code + pattern <- "`(renv::(?:[^`])+)`" + replacement <- "`\033]8;;x-r-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) + + } + bootstrap <- function(version, library) { + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + # attempt to download renv - tarball <- tryCatch(renv_bootstrap_download(version), error = identity) - if (inherits(tarball, "error")) - stop("failed to download renv ", version) + 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 - status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity) - if (inherits(status, "error")) - stop("failed to install renv ", version) + 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() { @@ -57,23 +250,32 @@ local({ 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)) + 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) - # if we're testing, re-use the test repositories - if (renv_bootstrap_tests_running()) - return(getOption("renv.tests.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@"] <- getOption( - "renv.repos.cran", - "https://cloud.r-project.org" - ) + repos[repos == "@CRAN@"] <- cran # add in renv.bootstrap.repos if set default <- c(FALLBACK = "https://cloud.r-project.org") @@ -86,31 +288,60 @@ local({ } + 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) { - # if the renv version number has 4 components, assume it must - # be retrieved via github - nv <- numeric_version(version) - components <- unclass(nv)[[1]] + sha <- attr(version, "sha", exact = TRUE) - methods <- if (length(components) == 4L) { - list( - renv_bootstrap_download_github + 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 { - list( - renv_bootstrap_download_cran_latest, - renv_bootstrap_download_cran_archive + + # 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(version), error = identity) + path <- tryCatch(method(), error = identity) if (is.character(path) && file.exists(path)) return(path) } - stop("failed to download renv ", version) + stop("All download methods failed") } @@ -126,43 +357,78 @@ local({ if (fixup) mode <- "w+b" - utils::download.file( + 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$headers <- headers + } + + do.call(utils::download.file, args) + } - renv_bootstrap_download_cran_latest <- function(version) { + renv_bootstrap_download_custom_headers <- function(url) { - spec <- renv_bootstrap_download_cran_latest_find(version) + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") - message("* Downloading renv ", version, " ... ", appendLF = FALSE) + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) type <- spec$type repos <- spec$repos - info <- tryCatch( - utils::download.packages( - pkgs = "renv", - destdir = tempdir(), - repos = repos, - type = type, - quiet = TRUE - ), + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), condition = identity ) - if (inherits(info, "condition")) { - message("FAILED") + if (inherits(status, "condition")) return(FALSE) - } # report success and return - message("OK (downloaded ", type, ")") - info[1, 2] + destfile } @@ -181,10 +447,21 @@ local({ for (type in types) { for (repos in renv_bootstrap_repos()) { + # build arguments for utils::available.packages() call + args <- list(type = type, repos = repos) + + # add custom headers if available -- note that + # utils::available.packages() will pass this to download.file() + if ("headers" %in% names(formals(utils::download.file))) { + headers <- renv_bootstrap_download_custom_headers(repos) + if (length(headers) && is.character(headers)) + args$headers <- headers + } + # retrieve package database db <- tryCatch( as.data.frame( - utils::available.packages(type = type, repos = repos), + do.call(utils::available.packages, args), stringsAsFactors = FALSE ), error = identity @@ -218,8 +495,6 @@ local({ urls <- file.path(repos, "src/contrib/Archive/renv", name) destfile <- file.path(tempdir(), name) - message("* Downloading renv ", version, " ... ", appendLF = FALSE) - for (url in urls) { status <- tryCatch( @@ -227,18 +502,55 @@ local({ condition = identity ) - if (identical(status, 0L)) { - message("OK") + if (identical(status, 0L)) return(destfile) - } } - message("FAILED") 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") @@ -246,23 +558,24 @@ local({ return(FALSE) # prepare download options - pat <- Sys.getenv("GITHUB_PAT") - if (nzchar(Sys.which("curl")) && nzchar(pat)) { + token <- renv_bootstrap_github_token() + if (is.null(token)) + token <- "" + + if (nzchar(Sys.which("curl")) && nzchar(token)) { fmt <- "--location --fail --header \"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + 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(pat)) { + } else if (nzchar(Sys.which("wget")) && nzchar(token)) { fmt <- "--header=\"Authorization: token %s\"" - extra <- sprintf(fmt, pat) + 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) } - message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE) - url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) name <- sprintf("renv_%s.tar.gz", version) destfile <- file.path(tempdir(), name) @@ -272,48 +585,129 @@ local({ condition = identity ) - if (!identical(status, 0L)) { - message("FAILED") + if (!identical(status, 0L)) return(FALSE) - } - message("OK") + 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 - message("* Installing renv ", version, " ... ", appendLF = FALSE) 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", "-l", shQuote(library), shQuote(tarball)) - output <- system2(r, args, stdout = TRUE, stderr = TRUE) - message("Done!") + R <- file.path(bin, exe) - # check for successful install - status <- attr(output, "status") - if (is.numeric(status) && !identical(status, 0L)) { - header <- "Error installing renv:" - lines <- paste(rep.int("=", nchar(header)), collapse = "") - text <- c(header, lines, output) - writeLines(text, con = stderr()) - } + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) - status + system2(R, args, stdout = TRUE, stderr = TRUE) } - renv_bootstrap_platform_prefix <- function() { + renv_bootstrap_platform_prefix_default <- function() { - # construct version prefix - version <- paste(R.version$major, R.version$minor, sep = ".") - prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + # read version component + version <- Sys.getenv("RENV_PATHS_VERSION", unset = "R-%v") + + # expand placeholders + placeholders <- list( + list("%v", format(getRversion()[1, 1:2])), + list("%V", format(getRversion()[1, 1:3])) + ) + + for (placeholder in placeholders) + version <- gsub(placeholder[[1L]], placeholder[[2L]], version, fixed = TRUE) # include SVN revision for development versions of R # (to avoid sharing platform-specific artefacts with released versions of R) @@ -322,10 +716,19 @@ local({ identical(R.version[["nickname"]], "Unsuffered Consequences") if (devel) - prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + version <- paste(version, R.version[["svn rev"]], sep = "-r") + + version + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- renv_bootstrap_platform_prefix_default() # build list of path components - components <- c(prefix, R.version$platform) + components <- c(version, R.version$platform) # include prefix if provided by user prefix <- renv_bootstrap_platform_prefix_impl() @@ -346,6 +749,9 @@ local({ # 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()) @@ -485,49 +891,97 @@ local({ renv_bootstrap_library_root <- function(project) { + prefix <- renv_bootstrap_profile_prefix() + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) if (!is.na(path)) - return(path) + return(paste(c(path, prefix), collapse = "/")) - path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) - if (!is.na(path)) { + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { name <- renv_bootstrap_library_root_name(project) - return(file.path(path, name)) + return(paste(c(path, prefix, name), collapse = "/")) } - prefix <- renv_bootstrap_profile_prefix() - paste(c(project, prefix, "renv/library"), collapse = "/") + renv_bootstrap_paths_renv("library", project = project) } - renv_bootstrap_validate_version <- function(version) { + 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) - loadedversion <- utils::packageDescription("renv", fields = "Version") - if (version == loadedversion) + if (valid) return(TRUE) - # assume four-component versions are from GitHub; three-component - # versions are from CRAN - components <- strsplit(loadedversion, "[.-]")[[1]] - remote <- if (length(components) == 4L) - paste("rstudio/renv", loadedversion, sep = "@") + # 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", loadedversion, sep = "@") + paste("renv", description[["Version"]], sep = "@") - fmt <- paste( - "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$s into the project library.", - sep = "\n" + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] ) - msg <- sprintf(fmt, loadedversion, version, remote) - warning(msg, call. = FALSE) + fmt <- heredoc(" + renv %1$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"]] + if (!is.character(expected)) + return(FALSE) + + pattern <- sprintf("^\\Q%s\\E", version) + grepl(pattern, expected, perl = TRUE) + + } + + 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-") @@ -547,6 +1001,12 @@ local({ # 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) @@ -562,7 +1022,7 @@ local({ return(profile) # check for a profile file (nothing to do if it doesn't exist) - path <- file.path(project, "renv/local/profile") + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) if (!file.exists(path)) return(NULL) @@ -573,7 +1033,7 @@ local({ # set RENV_PROFILE profile <- contents[[1L]] - if (nzchar(profile)) + if (!profile %in% c("", "default")) Sys.setenv(RENV_PROFILE = profile) profile @@ -583,7 +1043,7 @@ local({ renv_bootstrap_profile_prefix <- function() { profile <- renv_bootstrap_profile_get() if (!is.null(profile)) - return(file.path("renv/profiles", profile)) + return(file.path("profiles", profile, "renv")) } renv_bootstrap_profile_get <- function() { @@ -607,6 +1067,252 @@ local({ 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(project, libpath, version) + } + + renv_bootstrap_run <- function(project, libpath, version) { + + # 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 = project)) + } + + # 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_patterns <- function() { + + list( + + # objects + list("{", "\t\n\tobject(\t\n\t", TRUE), + list("}", "\t\n\t)\t\n\t", TRUE), + + # arrays + list("[", "\t\n\tarray(\t\n\t", TRUE), + list("]", "\n\t\n)\n\t\n", TRUE), + + # maps + list(":", "\t\n\t=\t\n\t", TRUE), + + # newlines + list("\\u000a", "\n", FALSE) + + ) + + } + + renv_json_read_envir <- function() { + + envir <- new.env(parent = emptyenv()) + + envir[["+"]] <- `+` + envir[["-"]] <- `-` + + envir[["object"]] <- function(...) { + result <- list(...) + names(result) <- as.character(names(result)) + result + } + + envir[["array"]] <- list + + envir[["true"]] <- TRUE + envir[["false"]] <- FALSE + envir[["null"]] <- NULL + + envir + + } + + renv_json_read_remap <- function(object, patterns) { + + # repair names if necessary + if (!is.null(names(object))) { + + nms <- names(object) + for (pattern in patterns) + nms <- gsub(pattern[[2L]], pattern[[1L]], nms, fixed = TRUE) + names(object) <- nms + + } + + # repair strings if necessary + if (is.character(object)) { + for (pattern in patterns) + object <- gsub(pattern[[2L]], pattern[[1L]], object, fixed = TRUE) + } + + # recurse for other objects + if (is.recursive(object)) + for (i in seq_along(object)) + object[i] <- list(renv_json_read_remap(object[[i]], patterns)) + + # return remapped object + object + + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # read json text + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + + # convert into something the R parser will understand + patterns <- renv_json_read_patterns() + transformed <- text + for (pattern in patterns) + transformed <- gsub(pattern[[1L]], pattern[[2L]], transformed, fixed = TRUE) + + # parse it + rfile <- tempfile("renv-json-", fileext = ".R") + on.exit(unlink(rfile), add = TRUE) + writeLines(transformed, con = rfile) + json <- parse(rfile, keep.source = FALSE, srcfile = NULL)[[1L]] + + # evaluate in safe environment + result <- eval(json, envir = renv_json_read_envir()) + + # fix up strings if necessary -- do so only with reversible patterns + patterns <- Filter(function(pattern) pattern[[3L]], patterns) + renv_json_read_remap(result, patterns) + + } + # load the renv profile, if any renv_bootstrap_profile_load(project) @@ -620,35 +1326,9 @@ local({ # construct full libpath libpath <- file.path(root, prefix) - # attempt to load - if (renv_bootstrap_load(project, libpath, version)) - return(TRUE) - - # load failed; inform user we're about to bootstrap - prefix <- paste("# Bootstrapping renv", version) - postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "") - header <- paste(prefix, postfix) - message(header) - - # 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)) { - message("* Successfully installed and loaded renv ", version, ".") - return(renv::load()) - } - - # 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." - ) + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) - warning(paste(msg, collapse = "\n"), call. = FALSE) + invisible() })