@r-universe/webr 2023.6.11 → 2023.6.21

package/dist/vfs/usr/lib/R/library/utils/tests/swv-keepSrc-1.Rnw

@@ -0,0 +1,48 @@
+\documentclass{article}
+\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,strip.white=true,keep.source=TRUE}
+
+\usepackage{Sweave}
+
+\begin{document}
+<<preliminaries, echo=FALSE, results=hide>>=
+options(width=70, useFancyQuotes = FALSE, prompt="R> ", continue="+  ")
+@
+\subsection*{Introduction}
+
+We generate 3D gaussian data,
+We generate 3D Gaussian data,
+<<ex1-U3>>=
+set.seed(1)
+n <- 100
+x <- rnorm(n); y <- 2*x + rnorm(n)/2
+U3 <- cbind(x, y, z = -3*x + y + rnorm(n)/4)
+@
+look at its structure
+<<str>>=
+str(U3) # its structure ((comment kept))
+@
+and load package \texttt{lattice}
+<<req-lattice>>=
+if(!require("lattice", quietly = TRUE)) q("no")
+@
+to visualize it by a simple scatter plot matrix
+\begin{figure}[h!]
+\centering
+<<splom-def, eval=false>>=
+splom(U3, xlab ="", cex = 0.4)
+<<splom, echo=FALSE, fig=TRUE, height=5>>=
+print(
+<<splom-def>>
+     )
+@
+\caption{\Sexpr{n} vectors of random variates ... ...}
+\label{fig:AC_Joe}
+\end{figure}
+
+\subsection*{Session Information}
+
+<<sessionInfo, results=tex>>=
+toLatex(sessionInfo())
+@
+
+\end{document}

package/dist/vfs/usr/lib/R/share/R/REMOVE.R

@@ -0,0 +1,82 @@
+#  File share/R/REMOVE.R
+#  Part of the R package, https://www.R-project.org
+#
+#  Copyright (C) 1995-2023 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  https://www.r-project.org/Licenses/
+
+Usage <- function() {
+    cat("Usage: R CMD REMOVE [options] pkgs",
+        "",
+        "Remove the add-on packages specified by pkgs.  The library tree to",
+        "remove from can be specified via '--library'.  By default, packages are",
+        "removed from the library tree rooted at the first directory in",
+        ".libPaths() for an R session run in the current environment.",
+        "",
+        "Options:",
+        "  -h, --help		print short help message and exit",
+        "  -v, --version		print REMOVE version info and exit",
+        "  -l, --library=LIB	remove packages from library tree LIB",
+        "",
+        "Report bugs at <https://bugs.R-project.org>.", sep="\n")
+}
+
+options(showErrorCalls = FALSE, warn = 1) # deferred warnings will not be seen
+pkgs <- character(0)
+lib <- ""
+args <- commandArgs(TRUE)
+while(length(args)) {
+    a <- args[1]
+    if(a %in% c("-h", "--help")) {
+        Usage()
+        q("no")
+    }
+    else if(a %in% c("-v", "--version")) {
+        cat("R add-on package remover: ",
+            R.version[["major"]], ".",  R.version[["minor"]],
+            " (r", R.version[["svn rev"]], ")\n", sep = "")
+        cat("",
+            tools:::.R_copyright_msg(2000),
+            "This is free software; see the GNU General Public License version 2",
+            "or later for copying conditions.  There is NO warranty.",
+            sep="\n")
+        q("no")
+    }
+    else if(a == "-l") {
+        if(length(args) >= 2) {lib <- args[2]; args <- args[-1]}
+        else stop("-l option without value", call. = FALSE)
+    } else if(substr(a, 1, 10) == "--library=")
+        lib <- substr(a, 11, 1000)
+    else pkgs <- c(pkgs, a)
+    args <- args[-1]
+}
+if(!length(pkgs))
+    stop("ERROR: no packages specified", call.=FALSE)
+if(!nzchar(lib)) {
+    lib <- .libPaths()[1]
+    message("Removing from library ", sQuote(lib))
+} else {
+    ## lib is allowed to be a relative path.
+    ## should be OK below, but be sure.
+    cwd <- try(setwd(path.expand(lib)), silent = TRUE)
+    if(inherits(cwd, "try-error"))
+        stop("ERROR: cannot cd to directory ", sQuote(lib), call. = FALSE)
+    lib <- getwd()
+    setwd(cwd)
+}
+if(!utils::file_test("-d", lib) || file.access(lib, 2L))
+    stop("ERROR: no permission to remove from directory ", sQuote(lib),
+         call. = FALSE)
+utils::remove.packages(pkgs, lib)
+q("no")

package/dist/vfs/usr/lib/R/share/R/examples-footer.R

@@ -0,0 +1,12 @@
+### * <FOOTER>
+###
+cleanEx()
+options(digits = 7L)
+base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
+grDevices::dev.off()
+###
+### Local variables: ***
+### mode: outline-minor ***
+### outline-regexp: "\\(> \\)?### [*]+" ***
+### End: ***
+quit('no')

package/dist/vfs/usr/lib/R/share/R/examples-header.R

@@ -0,0 +1,85 @@
+### * <HEADER>
+###
+attach(NULL, name = "CheckExEnv")
+assign("nameEx",
+       local({
+	   s <- "__{must remake R-ex/*.R}__"
+           function(new) {
+               if(!missing(new)) s <<- new else s
+           }
+       }),
+       pos = "CheckExEnv")
+## Add some hooks to label plot pages for base and grid graphics
+assign("base_plot_hook",
+       function() {
+           pp <- graphics::par(c("mfg","mfcol","oma","mar"))
+           if(all(pp$mfg[1:2] == c(1, pp$mfcol[2]))) {
+               outer <- (oma4 <- pp$oma[4]) > 0; mar4 <- pp$mar[4]
+               graphics::mtext(sprintf("help(\"%s\")", nameEx()), side = 4,
+                     line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1),
+               outer = outer, adj = 1, cex = 0.8, col = "orchid", las = 3)
+           }
+       },
+       pos = "CheckExEnv")
+assign("grid_plot_hook",
+       function() {
+           grid::pushViewport(grid::viewport(width=grid::unit(1, "npc") -
+                              grid::unit(1, "lines"), x=0, just="left"))
+           grid::grid.text(sprintf("help(\"%s\")", nameEx()),
+                           x=grid::unit(1, "npc") + grid::unit(0.5, "lines"),
+                           y=grid::unit(0.8, "npc"), rot=90,
+                           gp=grid::gpar(col="orchid"))
+       },
+       pos = "CheckExEnv")
+setHook("plot.new",     get("base_plot_hook", pos = "CheckExEnv"))
+setHook("persp",        get("base_plot_hook", pos = "CheckExEnv"))
+setHook("grid.newpage", get("grid_plot_hook", pos = "CheckExEnv"))
+assign("cleanEx",
+       function(env = .GlobalEnv) {
+	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+           RNGkind("default", "default", "default")
+	   set.seed(1)
+   	   options(warn = 1)
+	   .CheckExEnv <- as.environment("CheckExEnv")
+	   delayedAssign("T", stop("T used instead of TRUE", domain = NA),
+		  assign.env = .CheckExEnv)
+	   delayedAssign("F", stop("F used instead of FALSE", domain = NA),
+		  assign.env = .CheckExEnv)
+	   sch <- search()
+	   newitems <- sch[! sch %in% .oldSearch]
+           if(length(newitems)) tools:::detachPackages(newitems)
+	   missitems <- .oldSearch[! .oldSearch %in% sch]
+	   if(length(missitems))
+	       warning(sprintf("items %s were removed from the search path",
+                               paste(sQuote(missitems), collapse=", ")),
+                       call. = FALSE, immediate. = TRUE, domain = NA)
+           ## Old massaged files will not have set .old_wd.
+           if(exists(".old_wd") && (wd <- getwd()) != .old_wd) {
+               warning(sprintf("working directory was changed to %s, resetting",
+                               sQuote(wd)),
+                       call. = FALSE, immediate. = TRUE, domain = NA)
+               setwd(.old_wd)
+           }
+           ## stop in case users left connections open,
+           ## also indicating that parallel cluster are still running
+           if(Sys.getenv("_R_CHECK_CONNECTIONS_LEFT_OPEN_", FALSE)){
+               sC <- showConnections()
+               if(nrow(sC)){
+                   stop("connections left open:\n",
+                       paste(apply(sC[,1:2, drop = FALSE], 1L, function(x)
+                           paste0("\t", x[1L], " (", x[2L], ")")), collapse="\n"),
+				       call. = FALSE, domain = NA)
+               }
+           }
+       },
+       pos = "CheckExEnv")
+assign("ptime", proc.time(), pos = "CheckExEnv")
+## Do this before loading the package,
+## since packages have been known to change settings.
+## Force a size that is close to on-screen devices, fix paper.
+## don't rename par.postscript for back-compatibility of reference output.
+grDevices::pdf.options(width = 7, height = 7, paper = "special", reset = TRUE)
+grDevices::pdf(paste(pkgname, "-Ex.pdf", sep=""), encoding = "ISOLatin1")
+
+assign("par.postscript", graphics::par(no.readonly = TRUE), pos = "CheckExEnv")
+options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))

package/dist/vfs/usr/lib/R/share/R/nspackloader.R

@@ -0,0 +1,27 @@
+#  File share/R/nspackloader.R
+#  Part of the R package, https://www.R-project.org
+#
+#  Copyright (C) 1995-2012 The R Core Team
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  A copy of the GNU General Public License is available at
+#  https://www.r-project.org/Licenses/
+
+local({
+    info <- loadingNamespaceInfo()
+    pkg <- info$pkgname
+    ns <- .getNamespace(as.name(pkg))
+    if (is.null(ns))
+        stop("cannot find namespace environment for ", pkg, domain = NA);
+    dbbase <- file.path(info$libname, pkg, "R", pkg)
+    lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
+})

package/dist/vfs/usr/lib/R/share/R/tests-startup.R

@@ -0,0 +1,4 @@
+## A custom startup file for tests
+## Run as if a system Rprofile, so no packages, no assignments
+options(useFancyQuotes = FALSE)
+

package/dist/vfs/usr/lib/R/share/Rd/macros/system.Rd

@@ -0,0 +1,56 @@
+% System Rd macros
+
+% These macros are automatically loaded whenever R processes an Rd file.
+
+% Packages may define their own macros, which are stored in man/macros/*.Rd in
+% the source, help/macros/*.Rd after installation.  Those will be processed after
+% this file but before every Rd file in a package.
+
+% Packages may request inclusion of macros from other packages using the 
+% LoadRdMacros line in the DESCRIPTION file, e.g.
+%  LoadRdMacros:  pkgA 
+% These are loaded after the system macros and before the current package macros.
+
+% Individual Rd files may define their own macros.
+
+
+
+% To refer to a package on CRAN
+\newcommand{\CRANpkg}{\href{https://CRAN.R-project.org/package=#1}{\pkg{#1}}}
+
+% To refer to a bug report by number
+\newcommand{\PR}{\Sexpr[results=rd]{tools:::Rd_expr_PR(#1)}}
+
+% To avoid a double space after a period in LaTeX output
+\newcommand{\sspace}{\ifelse{latex}{\out{~}}{ }}
+
+% To get the package title at build time from the DESCRIPTION file
+\newcommand{\packageTitle}{\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("#1")}}
+
+% To get the package description at build time from the DESCRIPTION file
+\newcommand{\packageDescription}{\Sexpr[results=rd,stage=build]{tools:::Rd_package_description("#1")}}
+
+% To get the package author at build time from the DESCRIPTION file
+\newcommand{\packageAuthor}{\Sexpr[results=rd,stage=build]{tools:::Rd_package_author("#1")}}
+
+% To get the package maintainer at build time from the DESCRIPTION file
+\newcommand{\packageMaintainer}{\Sexpr[results=rd,stage=build]{tools:::Rd_package_maintainer("#1")}}
+
+% To get a formatted copy of the whole DESCRIPTION file
+\newcommand{\packageDESCRIPTION}{\Sexpr[results=rd,stage=build]{tools:::Rd_package_DESCRIPTION("#1")}}
+
+% To include various indices about an installed package
+
+\newcommand{\packageIndices}{\Sexpr[results=rd,stage=build]{tools:::Rd_package_indices("#1")}}
+
+% To indicate a DOI.
+\newcommand{\doi}{\Sexpr[results=rd]{tools:::Rd_expr_doi("#1")}}
+
+% To indicate LaTeX.
+\newcommand{\LaTeX}{\ifelse{latex}{\out{{\LaTeX}}}{LaTeX}}
+
+% To indicate a programming language.
+% Ideally this would also do something like
+%   \ifelse{html}{\out{<span style="font-family: sans-serif;">#1</span>}}
+% but this does not always work correctly with Rd2HTML() as of 2018-05.
+\newcommand{\proglang}{\ifelse{latex}{\out{\textsf{#1}}}{#1}}