Fix R CMD check errors/warnings

.Rbuildignore

@@ -3,3 +3,4 @@
 ^LICENSE\.md$
 notebooks
 reports
+releases

DESCRIPTION

@@ -50,12 +50,16 @@ Imports:
     keyring,
     getPass,
     sodium (>= 1.1),
-    Rcpp (>= 1.0.8),
     qs (>= 0.25),
-    cyphr,
     stringr,
+    dplyr,
+    rlang,
+    tibble,
+    magrittr,
     shiny,
+    shinydashboard,
     shinythemes,
+    htmltools,
     markdown
 Depends:
     R (>= 4.1.0),

NAMESPACE

@@ -22,19 +22,26 @@ export(gy_unzip)
 export(gy_users)
 export(gy_zip)
 export(run_app)
+import(magrittr)
 import(shiny)
 import(shinydashboard)
 importFrom(base64enc,base64decode)
 importFrom(base64enc,base64encode)
+importFrom(dplyr,arrange)
+importFrom(dplyr,mutate)
 importFrom(getPass,getPass)
+importFrom(htmltools,includeMarkdown)
 importFrom(keyring,key_delete)
 importFrom(keyring,key_get)
 importFrom(keyring,key_list)
 importFrom(keyring,key_set_with_value)
+importFrom(markdown,mark)
 importFrom(qs,qdeserialize)
 importFrom(qs,qserialize)
+importFrom(rlang,.data)
 importFrom(rstudioapi,isAvailable)
 importFrom(rstudioapi,selectDirectory)
+importFrom(shinythemes,shinytheme)
 importFrom(sodium,auth_decrypt)
 importFrom(sodium,auth_encrypt)
 importFrom(sodium,data_decrypt)
@@ -49,8 +56,12 @@ importFrom(sodium,sig_verify)
 importFrom(sodium,simple_decrypt)
 importFrom(sodium,simple_encrypt)
 importFrom(stringr,str_c)
+importFrom(stringr,str_detect)
 importFrom(stringr,str_glue)
 importFrom(stringr,str_remove)
+importFrom(stringr,str_split)
+importFrom(tibble,as_tibble)
+importFrom(utils,download.file)
 importFrom(zip,unzip)
 importFrom(zip,zip)
 importFrom(zip,zip_list)

R/get_localuser.R

@@ -1,3 +1,8 @@
+#' @importFrom utils download.file
+#' @importFrom stringr str_detect str_split
+#' @importFrom tibble as_tibble
+#' @importFrom dplyr mutate arrange
+
 get_localuser <- function(){
   if(is.null(package_env$currentlocal)) gy_profile()
 

R/goldeneye-package.R

@@ -1,3 +1,6 @@
+#' @importFrom shinythemes shinytheme
+#' @importFrom htmltools includeMarkdown
+#' @importFrom markdown mark
 #' @keywords internal
 "_PACKAGE"
 

R/gy_check.R

@@ -4,6 +4,8 @@
 #' @param path path to goldeneye profile
 #' @param silent option to suppress output to screen
 #'
+#' @importFrom rlang .data
+#' @import magrittr
 
 #' @rdname gy_profile
 #' @export
@@ -62,8 +64,8 @@ gy_info <- function(silent=FALSE){
         c(unlist(x[c("user","name","email")]), member_since=as.character(x$member_since))
       }, character(4))) %>%
         as_tibble() %>%
-        mutate(member_since=as.Date(member_since)) %>%
-        arrange(member_since)
+        mutate(member_since=as.Date(.data$member_since)) %>%
+        arrange(.data$member_since)
       if(redact) usrs$email <- "**@**.**"
       print(usrs)
     }
@@ -94,8 +96,8 @@ gy_info <- function(silent=FALSE){
         c(unlist(x[c("user","name","email")]), member_since=as.character(x$member_since))
       }, character(4))) %>%
         as_tibble() %>%
-        mutate(member_since=as.Date(member_since)) %>%
-        arrange(member_since)
+        mutate(member_since=as.Date(.data$member_since)) %>%
+        arrange(.data$member_since)
       if(redact) usrs$email <- "**@**.**"
       print(usrs)
     }

R/gy_create_group.R

@@ -18,7 +18,7 @@ gy_create_group <- function(group, weblink, password){
 
 
   weblink <- readRDS(getOption("goldeneye_path"))$groups$goldfinger$weblink
-  webinfo <- goldeneye:::refresh_users(weblink)
+  webinfo <- refresh_users(weblink)
   user_info <- webinfo$users
   names(user_info)
 
@@ -47,18 +47,19 @@ gy_create_group <- function(group, weblink, password){
 
   users <- list(usernames=usernames, user_info=sodium::data_encrypt(serialize(user_info, NULL), sodium::hash(charToRaw(webpwd))), message=sodium::data_encrypt(serialize(msg, NULL), sodium::hash(charToRaw(webpwd))), public_curve=public_curve, public_ed=public_ed)
 
-  verification <- goldeneye:::gy_sign(users)
+  verification <- gy_sign(users)
 
   versions <- attr(verification, "versions")
   versions["type"] <- "generic"
   versions["minimum"] <- "0.5.0-1"
   attr(verification, "versions") <- versions
-  stopifnot(goldeneye:::gy_verify(users, verification, silent=TRUE))
+  stopifnot(gy_verify(users, verification, silent=TRUE))
   attr(verification, "user") <- NULL
 
   keys <- list(group="demo22", users=users, verification=verification)
   saveRDS(keys, "demo22.gyg", compress=FALSE)
 
+  webpwd <- NULL
   weblink <- str_c("https://www.costmodds.org/rsc/goldeneye/demo22.gyg#",webpwd,"#md")
 
 

R/gy_encrypt.R

@@ -5,6 +5,8 @@
 #' @param local_user should the current user also be able to decrypt thw file?
 #' @param comment an optional comment that will be sent (unencrypted) along with the file
 #' @param funs optional additional encryption steps: this must be the output of a call to \code{\link{gy_key_funs}}
+#' @param run_custom should any custom decryption functions be run automatically?
+#' @param type the type of public key to return ("curve" or "ed")
 #'
 #' @rdname gy_encrypt
 #' @export

R/gy_join_group.R

@@ -1,9 +1,10 @@
 #' @name gy_join_group
 #' @title Join an existing goldeneye user group via a weblink
-#'
-#'
 #' @param weblink the weblink as provided by the group administrator
 #' @param user the username that you want to use for this group
+#' @param make_default should this become the default group?
+#' @param group the name of the group to set
+#' @param silent option to silence output
 #'
 #' @importFrom stringr str_glue
 #'
@@ -44,7 +45,7 @@ gy_join_group <- function(weblink=NULL, user=NULL, make_default=FALSE){
   }else if(!is.null(local$user)){
     tuser <- local$user
   }else if(!is.na(local$groups$default_group)){
-    if(!default_group %in% names(local$group)){
+    if(!"default_group" %in% names(local$group)){
       stop("An unexpected error occured with the groups element of your user profile: please contact the package maintaner with this error message for help")
     }
     tuser <- local$groups[[local$groups$default_group]][["user"]]

R/gy_key_funs.R

@@ -1,11 +1,8 @@
-#' Title
+#' Obtain key functions
 #'
-#' @param type
+#' @param type type of key function (only "identity" is currently supported)
 #'
-#' @return
 #' @export
-#'
-#' @examples
 gy_key_funs <- function(type){
 
   stopifnot(type=="identity")

R/gy_public_file.R

@@ -1,7 +1,7 @@
-#' Title
+#' Extract the public key file
 #'
-#' @param file
-#' @param silent
+#' @param file filename to write to
+#' @param silent do this quietly?
 #'
 #' @export
 gy_public_file <- function(file="goldeneye_public.gyu", silent=FALSE){

R/gy_saveRDS.R

@@ -1,13 +1,16 @@
 #' @name gf_saveRDS
 #' @title Save and read encrypted RDS
-#' @param object
-#' @param file
-#' @param user
-#' @param local_user
-#' @param ascii
-#' @param version
-#' @param compress
-#' @param overwrite
+#'
+#' @param object the object to encrypt
+#' @param file the filename to which the encrypted object will be saved
+#' @param users one or more users who will be authorised to decrypt the file
+#' @param local_user should the local user be able to decrypt the file?
+#' @param comment a comment to include
+#' @param overwrite should the file be overwritten, if it exists?
+#' @param ascii argument passed to saveRDS
+#' @param funs argument passed to saveRDS
+#' @param ... arguments passed to gy_serialise
+#' @param run_custom should any custom decryption functions be run automatically?
 #'
 #' @rdname gy_saveRDS
 #' @export

R/gy_serialise.R

@@ -1,13 +1,9 @@
 #' @name gy_serialise
 #' @title Serialise and deserialise a list of objects/files
-#' @param object
-#' @param file
-#' @param user
-#' @param local_user
-#' @param ascii
-#' @param version
-#' @param compress
-#' @param overwrite
+#' @param object the object to encrypt
+#' @param files external files to serialise (not yet implemented)
+#' @param method the serialisation method to use (base, qs, or custom)
+#' @param ... arguments passed to the underlying serialisation method
 #'
 #' @importFrom qs qserialize qdeserialize
 #'

R/gy_setup.R

@@ -1,4 +1,11 @@
-#' Title
+#' Setup a new goldeyene encryption profile
+#'
+#' @param name your full name
+#' @param email your email address
+#' @param filename the filename to which the profile will be saved
+#' @param path the path in which to save the profile
+#' @param append_Rprofile should the R profile file be appended to automatically load this profile when R is restarted?
+#' @param silent option to suppress output
 #'
 #' @importFrom stringr str_remove str_c
 #' @importFrom getPass getPass

R/gy_users.R

@@ -1,12 +1,9 @@
-#' Title
+#' Obtain a list of users for a given group
 #'
-#' @param group
-#' @param refresh
+#' @param group the group for which to return users (defaults to the active group)
+#' @param refresh should the list be refreshed from the remote/online location?
 #'
-#' @return
 #' @export
-#'
-#' @examples
 gy_users <- function(group=NULL, refresh=FALSE){
 
   if(is.null(package_env$currentlocal)) gy_profile(silent=TRUE)
@@ -27,8 +24,8 @@ gy_users <- function(group=NULL, refresh=FALSE){
     c(unlist(x[c("user","name","email")]), member_since=as.character(x$member_since))
     }, character(4))) %>%
     as_tibble() %>%
-    mutate(member_since=as.Date(member_since)) %>%
-    arrange(member_since)
+    mutate(member_since=as.Date(.data$member_since)) %>%
+    arrange(.data$member_since)
 
   if(redact) usrs$email <- "**@**.**"
 

R/gy_zip.R

@@ -1,11 +1,16 @@
 #' @name gy_zip
 #' @title Zip and encrypt external files using goldeneye
-#' @param files one or more files to add to the zip archive
+#' @param input_files one or more files to add to the zip archive
+#' @param file the filename to which the encrypted object will be saved
 #' @param compression_level compression level to use on a scale of 1-9 (passed to \code{\link[zip]{zip}})
 #' @param users a character vector of (other) users within your current user group for whom the encrypted file will be decryptable. Alternatively, this can be a vector of paths/urls to public keys, or a mixture of the two.
 #' @param local_user should the current user also be able to decrypt thw file?
 #' @param comment an optional comment that will be sent (unencrypted) along with the file
 #' @param funs optional additional encryption steps: this must be the output of a call to \code{\link{gy_key_funs}}
+#' @param directory the directory to which the decrypted/unzipped files will be saved
+#' @param unzip should the decrypted files also be unzipped?
+#' @param overwrite should the file be overwritten, if it exists?
+#' @param run_custom should any custom decryption functions be run automatically?
 #'
 #' @importFrom zip zip unzip zip_list
 #' @importFrom base64enc base64encode base64decode