add packrat

.Rbuildignore

@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.Rprofile$
+^packrat/

.Rprofile

@@ -0,0 +1,3 @@
+#### -- Packrat Autoloader (version 0.4.9-3) -- ####
+source("packrat/init.R")
+#### -- End Packrat Autoloader -- ####

.Rproj.user/C9AE6405/pcs/find-in-files.pper

@@ -4,7 +4,7 @@
         "filePatterns" : [
         ],
         "path" : "~",
-        "query" : "ASCII",
+        "query" : "var_id.rd",
         "regex" : false
     }
 }

.Rproj.user/C9AE6405/pcs/source-pane.pper

@@ -1,3 +1,3 @@
 {
-    "activeTab" : 0
+    "activeTab" : 2
 }

.Rproj.user/C9AE6405/pcs/windowlayoutstate.pper

@@ -1,14 +1,14 @@
 {
     "left" : {
-        "panelheight" : 675,
-        "splitterpos" : 204,
+        "panelheight" : 729,
+        "splitterpos" : 221,
         "topwindowstate" : "NORMAL",
-        "windowheight" : 748
+        "windowheight" : 803
     },
     "right" : {
-        "panelheight" : 675,
-        "splitterpos" : 260,
+        "panelheight" : 729,
+        "splitterpos" : 281,
         "topwindowstate" : "NORMAL",
-        "windowheight" : 748
+        "windowheight" : 803
     }
 }

.Rproj.user/C9AE6405/persistent-state

@@ -1,10 +1,11 @@
 activeClientUrl="https://argonaut.is.ed.ac.uk/s/3b4b3e1b2674a2ac72186/"
 build-last-errors="[]"
-build-last-errors-base-dir="~/impactr/"
-build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source impactr\\n\\n\",\"type\":0},{\"output\":\"* installing to library ‘/home/kmclean/R/x86_64-pc-linux-gnu-library/3.4’\\n\",\"type\":1},{\"output\":\"* installing *source* package ‘impactr’ ...\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** preparing package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"Warning: replacing previous import ‘dplyr::intersect’ by ‘lubridate::intersect’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"Warning: replacing previous import ‘dplyr::union’ by ‘lubridate::union’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"Warning: replacing previous import ‘dplyr::setdiff’ by ‘lubridate::setdiff’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"Warning: replacing previous import ‘magrittr::set_names’ by ‘purrr::set_names’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"\",\"type\":1},{\"output\":\"Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** copying figures\\n\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** installing vignettes\\n\",\"type\":1},{\"output\":\"** testing if installed package can be loaded\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"Warning: replacing previous import ‘dplyr::intersect’ by ‘lubridate::intersect’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"Warning: replacing previous import ‘dplyr::union’ by ‘lubridate::union’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"Warning: replacing previous import ‘dplyr::setdiff’ by ‘lubridate::setdiff’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"Warning: replacing previous import ‘magrittr::set_names’ by ‘purrr::set_names’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"Warning: replacing previous import ‘magrittr::extract’ by ‘tidyr::extract’ when loading ‘impactr’\\n\",\"type\":2},{\"output\":\"\",\"type\":1},{\"output\":\"* DONE (impactr)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
+build-last-errors-base-dir=""
+build-last-outputs="[]"
 compile_pdf_state="{\"errors\":[],\"output\":\"\",\"running\":false,\"tab_visible\":false,\"target_file\":\"\"}"
 files.monitored-path=""
 find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":true,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOff\":[],\"matchOn\":[]},\"running\":false}"
 imageDirtyState="0"
-portToken="c597faf203a3"
+packratEnabled="1"
+portToken="98c62d446885"
 saveActionState="0"

.Rproj.user/C9AE6405/sources/prop/E8A726A2

@@ -1,4 +1,4 @@
 {
-    "cursorPosition" : "28,12",
-    "scrollLine" : "10"
+    "cursorPosition" : "11,0",
+    "scrollLine" : "5"
 }

.Rproj.user/C9AE6405/sources/s-2ac72186/lock_file

@@ -1 +1 @@
-56016
+42801

.Rproj.user/shared/notebooks/paths

@@ -15,6 +15,7 @@
 /home/kmclean/collaborator/vignettes/vignette_summary.Rmd="EF3F5101"
 /home/kmclean/collaborator/vignettes/vignette_user_2_assign.Rmd="8E6C362"
 /home/kmclean/impactr/.Rbuildignore="D18365D3"
+/home/kmclean/impactr/.Rprofile="BD03410E"
 /home/kmclean/impactr/.gitignore="D609B0B1"
 /home/kmclean/impactr/DESCRIPTION="22AFEF46"
 /home/kmclean/impactr/NAMESPACE="CFE2FF95"
@@ -39,11 +40,6 @@
 /home/kmclean/impactr/R/score_alm.R="C0E2D5F6"
 /home/kmclean/impactr/README.md="49EA9396"
 /home/kmclean/impactr/man/comb_name_size.Rd="C7D70E07"
-/home/kmclean/impactr/vignettes/vignette_1_extract.Rmd="AB149A52"
-/home/kmclean/impactr/vignettes/vignette_2_cite.Rmd="3B9971DE"
-/home/kmclean/impactr/vignettes/vignette_3_traditional.Rmd="1578E6D7"
-/home/kmclean/impactr/vignettes/vignette_4_author.Rmd="2AB4D9BA"
-/home/kmclean/impactr/vignettes/vignette_5_altmetric.Rmd="9029258"
 /home/kmclean/starsurg_impact/app/impact/app.R="53B9CA75"
 /home/kmclean/starsurg_impact/app/impact/starsurg_altmetric.Rmd="ADC030BC"
 /home/kmclean/starsurg_impact/app/impact/starsurg_citation.Rmd="743B1039"

.Rproj.user/shared/users/2ac72186.lock

@@ -1 +1 @@
-56016
+42801

.Rproj.user/shared/users/2ac72186.user

@@ -1 +1 @@
-{"client_id":"5d8f7237-833a-4d7c-ab78-791223abf371","color":"#45e6b0","current_edit_id":"","currently_editing":"","last_seen":1581873308,"session_id":"2ac72186","time_since_last_seen":0,"username":"kmclean"}
+{"client_id":"cd962f00-5f96-4de4-899c-c1d83ddfcaa3","color":"#45e6b0","current_edit_id":"","currently_editing":"","last_seen":1581876691,"session_id":"2ac72186","time_since_last_seen":0,"username":"kmclean"}

.Ruserdata/kmclean/.Rhistory

@@ -1,7 +1,3 @@
-x$ISSN <-  x$ISSN[1]
-x$page <- paste(unique(x$page), collapse="-")
-df_na <- NULL
-if(length(extract_var[which(extract_var %ni% names(x))])>0){
 df_na <- rbind.data.frame(rep(NA, length(extract_var[which(extract_var %ni% names(x))])))
 colnames(df_na) <- extract_var[which(extract_var %ni% names(x))]}
 y <- tibble::as_tibble(x)
@@ -510,3 +506,7 @@ theme_bw(base_size = 13)
 ggsave(plot_cite_time, filename = "~/impactr/vignettes/plot/plot_cite_time.png",
 height = 5.76*0.75, width = 9.60*0.75)
 library(impactr)
+library(impactr)
+devtools::document()
+devtools::document()
+library(impactr)

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+packrat/lib*/

packrat/init.R

@@ -0,0 +1,226 @@
+local({
+
+  ## Helper function to get the path to the library directory for a
+  ## given packrat project.
+  getPackratLibDir <- function(projDir = NULL) {
+    path <- file.path("packrat", "lib", R.version$platform, getRversion())
+
+    if (!is.null(projDir)) {
+
+      ## Strip trailing slashes if necessary
+      projDir <- sub("/+$", "", projDir)
+
+      ## Only prepend path if different from current working dir
+      if (!identical(normalizePath(projDir), normalizePath(getwd())))
+        path <- file.path(projDir, path)
+    }
+
+    path
+  }
+
+  ## Ensure that we set the packrat library directory relative to the
+  ## project directory. Normally, this should be the working directory,
+  ## but we also use '.rs.getProjectDirectory()' if necessary (e.g. we're
+  ## rebuilding a project while within a separate directory)
+  libDir <- if (exists(".rs.getProjectDirectory"))
+    getPackratLibDir(.rs.getProjectDirectory())
+  else
+    getPackratLibDir()
+
+  ## Unload packrat in case it's loaded -- this ensures packrat _must_ be
+  ## loaded from the private library. Note that `requireNamespace` will
+  ## succeed if the package is already loaded, regardless of lib.loc!
+  if ("packrat" %in% loadedNamespaces())
+    try(unloadNamespace("packrat"), silent = TRUE)
+
+  if (suppressWarnings(requireNamespace("packrat", quietly = TRUE, lib.loc = libDir))) {
+
+    # Check 'print.banner.on.startup' -- when NA and RStudio, don't print
+    print.banner <- packrat::get_opts("print.banner.on.startup")
+    if (print.banner == "auto" && is.na(Sys.getenv("RSTUDIO", unset = NA))) {
+      print.banner <- TRUE
+    } else {
+      print.banner <- FALSE
+    }
+    return(packrat::on(print.banner = print.banner))
+  }
+
+  ## Escape hatch to allow RStudio to handle bootstrapping. This
+  ## enables RStudio to provide print output when automagically
+  ## restoring a project from a bundle on load.
+  if (!is.na(Sys.getenv("RSTUDIO", unset = NA)) &&
+      is.na(Sys.getenv("RSTUDIO_PACKRAT_BOOTSTRAP", unset = NA))) {
+    Sys.setenv("RSTUDIO_PACKRAT_BOOTSTRAP" = "1")
+    setHook("rstudio.sessionInit", function(...) {
+      # Ensure that, on sourcing 'packrat/init.R', we are
+      # within the project root directory
+      if (exists(".rs.getProjectDirectory")) {
+        owd <- getwd()
+        setwd(.rs.getProjectDirectory())
+        on.exit(setwd(owd), add = TRUE)
+      }
+      source("packrat/init.R")
+    })
+    return(invisible(NULL))
+  }
+
+  ## Bootstrapping -- only performed in interactive contexts,
+  ## or when explicitly asked for on the command line
+  if (interactive() || "--bootstrap-packrat" %in% commandArgs(TRUE)) {
+
+    needsRestore <- "--bootstrap-packrat" %in% commandArgs(TRUE)
+
+    message("Packrat is not installed in the local library -- ",
+            "attempting to bootstrap an installation...")
+
+    ## We need utils for the following to succeed -- there are calls to functions
+    ## in 'restore' that are contained within utils. utils gets loaded at the
+    ## end of start-up anyhow, so this should be fine
+    library("utils", character.only = TRUE)
+
+    ## Install packrat into local project library
+    packratSrcPath <- list.files(full.names = TRUE,
+                                 file.path("packrat", "src", "packrat")
+    )
+
+    ## No packrat tarballs available locally -- try some other means of installation
+    if (!length(packratSrcPath)) {
+
+      message("> No source tarball of packrat available locally")
+
+      ## There are no packrat sources available -- try using a version of
+      ## packrat installed in the user library to bootstrap
+      if (requireNamespace("packrat", quietly = TRUE) && packageVersion("packrat") >= "0.2.0.99") {
+        message("> Using user-library packrat (",
+                packageVersion("packrat"),
+                ") to bootstrap this project")
+      }
+
+      ## Couldn't find a user-local packrat -- try finding and using devtools
+      ## to install
+      else if (requireNamespace("devtools", quietly = TRUE)) {
+        message("> Attempting to use devtools::install_github to install ",
+                "a temporary version of packrat")
+        library(stats) ## for setNames
+        devtools::install_github("rstudio/packrat")
+      }
+
+      ## Try downloading packrat from CRAN if available
+      else if ("packrat" %in% rownames(available.packages())) {
+        message("> Installing packrat from CRAN")
+        install.packages("packrat")
+      }
+
+      ## Fail -- couldn't find an appropriate means of installing packrat
+      else {
+        stop("Could not automatically bootstrap packrat -- try running ",
+             "\"'install.packages('devtools'); devtools::install_github('rstudio/packrat')\"",
+             "and restarting R to bootstrap packrat.")
+      }
+
+      # Restore the project, unload the temporary packrat, and load the private packrat
+      if (needsRestore)
+        packrat::restore(prompt = FALSE, restart = TRUE)
+
+      ## This code path only reached if we didn't restart earlier
+      unloadNamespace("packrat")
+      requireNamespace("packrat", lib.loc = libDir, quietly = TRUE)
+      return(packrat::on())
+
+    }
+
+    ## Multiple packrat tarballs available locally -- try to choose one
+    ## TODO: read lock file and infer most appropriate from there; low priority because
+    ## after bootstrapping packrat a restore should do the right thing
+    if (length(packratSrcPath) > 1) {
+      warning("Multiple versions of packrat available in the source directory;",
+              "using packrat source:\n- ", shQuote(packratSrcPath))
+      packratSrcPath <- packratSrcPath[[1]]
+    }
+
+
+    lib <- file.path("packrat", "lib", R.version$platform, getRversion())
+    if (!file.exists(lib)) {
+      dir.create(lib, recursive = TRUE)
+    }
+
+    message("> Installing packrat into project private library:")
+    message("- ", shQuote(lib))
+
+    surround <- function(x, with) {
+      if (!length(x)) return(character())
+      paste0(with, x, with)
+    }
+
+
+    ## Invoke install.packages() in clean R session
+    peq <- function(x, y) paste(x, y, sep = " = ")
+    installArgs <- c(
+      peq("pkgs", surround(packratSrcPath, with = "'")),
+      peq("lib", surround(lib, with = "'")),
+      peq("repos", "NULL"),
+      peq("type", surround("source", with = "'"))
+    )
+
+    fmt <- "utils::install.packages(%s)"
+    installCmd <- sprintf(fmt, paste(installArgs, collapse = ", "))
+
+    ## Write script to file (avoid issues with command line quoting
+    ## on R 3.4.3)
+    installFile <- tempfile("packrat-bootstrap", fileext = ".R")
+    writeLines(installCmd, con = installFile)
+    on.exit(unlink(installFile), add = TRUE)
+
+    fullCmd <- paste(
+      surround(file.path(R.home("bin"), "R"), with = "\""),
+      "--vanilla",
+      "--slave",
+      "-f",
+      surround(installFile, with = "\"")
+    )
+    system(fullCmd)
+
+    ## Tag the installed packrat so we know it's managed by packrat
+    ## TODO: should this be taking information from the lockfile? this is a bit awkward
+    ## because we're taking an un-annotated packrat source tarball and simply assuming it's now
+    ## an 'installed from source' version
+
+    ## -- InstallAgent -- ##
+    installAgent <- "InstallAgent: packrat 0.4.9-3"
+
+    ## -- InstallSource -- ##
+    installSource <- "InstallSource: source"
+
+    packratDescPath <- file.path(lib, "packrat", "DESCRIPTION")
+    DESCRIPTION <- readLines(packratDescPath)
+    DESCRIPTION <- c(DESCRIPTION, installAgent, installSource)
+    cat(DESCRIPTION, file = packratDescPath, sep = "\n")
+
+    # Otherwise, continue on as normal
+    message("> Attaching packrat")
+    library("packrat", character.only = TRUE, lib.loc = lib)
+
+    message("> Restoring library")
+    if (needsRestore)
+      packrat::restore(prompt = FALSE, restart = FALSE)
+
+    # If the environment allows us to restart, do so with a call to restore
+    restart <- getOption("restart")
+    if (!is.null(restart)) {
+      message("> Packrat bootstrap successfully completed. ",
+              "Restarting R and entering packrat mode...")
+      return(restart())
+    }
+
+    # Callers (source-erers) can define this hidden variable to make sure we don't enter packrat mode
+    # Primarily useful for testing
+    if (!exists(".__DONT_ENTER_PACKRAT_MODE__.") && interactive()) {
+      message("> Packrat bootstrap successfully completed. Entering packrat mode...")
+      packrat::on()
+    }
+
+    Sys.unsetenv("RSTUDIO_PACKRAT_BOOTSTRAP")
+
+  }
+
+})