Cran 1.0.2 release (#64)

.circleci/config.yml

@@ -3,15 +3,6 @@
 # - Builds attempted for 3.6.3, 4.0.5, and the *latest* R edition supported by rocker.
 
 version: 2.1
-
-workflows:
-
-  version: 2
-  Prepare-All-R-Editions:
-    jobs:
-      - Build-for-r4_0_5
-      - Build-for-rLATEST
-
 jobs:
 
   Build-for-r4_0_5:
@@ -56,7 +47,6 @@ jobs:
             # Perform package check
             R CMD check *tar.gz
 
-
   Build-for-rLATEST:
     docker:
       - image: rocker/verse:latest
@@ -104,3 +94,9 @@ jobs:
             # Perform package check
             R CMD check *tar.gz
 
+workflows:
+  version: 2
+  Prepare-All-R-Editions:
+    jobs:
+      - Build-for-r4_0_5
+      - Build-for-rLATEST

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: periscope
 Type: Package
 Title: Enterprise Streamlined 'Shiny' Application Framework
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(
     person("Constance", "Brett", email="connie@aggregate-genius.com", role = c("aut", "cre")),
     person("Isaac", "Neuhaus", role = "aut", comment = "canvasXpress JavaScript Library Maintainer"),
@@ -33,7 +33,7 @@ Imports:
     fresh,
     yaml,
     grDevices
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Suggests:
     knitr,
     rmarkdown,

NEWS.md

@@ -1,5 +1,7 @@
 #Revisions and Change Log
 
+### v1.0.2
+* Minor bugfixes - handled classes and packageversion checking in compliance with latest R requirements to resolve notes
 
 ### v1.0.1
 * Minor bugfixes - updated font awesome icons (to v5 compatible)

R/downloadFile.R

@@ -274,7 +274,7 @@ download_file <- function(input,
         # excel file
         else if (type == "xlsx") {
             if ("openxlsx" %in% utils::installed.packages()) {
-                if ((class(data) == "Workbook") && ("openxlsx" %in% attributes(class(data)))) {
+                if (("Workbook" %in% class(data)) && ("openxlsx" %in% attributes(class(data)))) {
                     openxlsx::saveWorkbook(data, file)
                 } else {
                     show_rownames <- attr(data, "show_rownames")
@@ -288,7 +288,7 @@ download_file <- function(input,
         }
         # text file processing
         else if (type == "txt") {
-            if (class(data) == "character") {
+            if ("character" %in% class(data)) {
                 writeLines(data, file)
             }
             else if (is.data.frame(data) || is.matrix(data)) {

R/fw_helpers_external.R

@@ -164,7 +164,7 @@ fw_create_body <- function() {
     app_info <- shiny::isolate(.g_opts$app_info)
     info_content <- NULL
 
-    if (!is.null(app_info) && (class(app_info)[1] == "html")) {
+    if (!is.null(app_info) && ("html" %in% class(app_info))) {
         info_content <- shinyBS::bsModal(
                 id = "titleinfobox",
                 title = shiny::isolate(.g_opts$app_title),

R/fw_helpers_internal.R

@@ -49,7 +49,7 @@
             "$(\"<div class='periscope-title'>",
             ifelse(is.null(app_info),
                    app_title,
-                   ifelse(class(app_info)[1] == "html",
+                   ifelse("html" %in% class(app_info),
                           paste("<a id='titleinfobox_trigger' href='#'>",
                                 app_title, "</a>"),
                           paste("<a href='", app_info,

R/generate_template.R

@@ -139,9 +139,9 @@ create_new_application <- function(name,
         dashboard_plus <- FALSE
         right_sidebar_icon <- NULL
         if (!is.null(rightsidebar)) {
-            if (class(rightsidebar) == "logical") {
+            if ("logical" %in% class(rightsidebar)) {
                 if (rightsidebar) { dashboard_plus <- TRUE  }
-            } else if (class(rightsidebar) == "character") {
+            } else if ("character" %in% class(rightsidebar)) {
                 dashboard_plus <- TRUE
                 right_sidebar_icon <- rightsidebar
             } else {

R/periscope.R

@@ -45,7 +45,7 @@ NULL
 
 .onLoad <- function(libname, pkgname) {
     if (length(find.package('shinydashboardPlus', quiet = T)) > 0) {
-        if (utils::packageVersion('shinydashboardPlus') < 2) {
+        if (utils::packageVersion('shinydashboardPlus') < "2") {
             .g_sdp_oldver <<- TRUE
         }
         .g_sdp_installed <<- TRUE

README.md

@@ -11,7 +11,7 @@ output:
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/periscope?color=9bc2cf)](https://cran.r-project.org/package=periscope)
 [![CRAN_Downloads_Badge](https://cranlogs.r-pkg.org/badges/grand-total/periscope?color=9bc2cf)](https://cran.r-project.org/package=periscope)
 [![CircleCI](https://circleci.com/gh/cb4ds/periscope/tree/master.svg?style=shield)](https://app.circleci.com/pipelines/github/cb4ds/periscope?branch=master)
-[![Coverage Status](https://img.shields.io/codecov/c/github/cb4ds/periscope/master.svg)](https://codecov.io/github/cb4ds/periscope?branch=master)
+[![Coverage Status](https://img.shields.io/codecov/c/github/cb4ds/periscope/master.svg)](https://app.codecov.io/github/cb4ds/periscope?branch=master)
 <!-- End Badges -->
 
 ***periscope*** was originally developed as the core Shiny component for bioinformatics and systems biology analysis applications. It provides a predefined but flexible template for new Shiny applications with a default dashboard layout, three locations for user alerts, a nice busy indicator and logging features. 

cran-comments.md

@@ -1,26 +1,21 @@
 ## Comments from Maintainer
 
-Resubmission Comments:
-* permanent redirect for CircleCI was not caught, corrected the URL in the readme
-
-Original Comments:
-Minor bugfix release to update icons, templated examples
+Bugfixes for the changes in utils::packageVersion and class checks in the package and tests
 
 ---  
 
 ## Test Environments
 
 
-RStudio Server Pro (Ubuntu 18.04.2)  
-
-* R 3.6.3
+RStudio Server Pro (Ubuntu 20.04)
 * R 4.0.5
-* R 4.1.1
+* R 4.2.3
+* R 4.3.0
 
 CircleCI
 
 * R 4.0.5
-* R 4.1.2
+* R latest
 
 WinBuilder
 

inst/fw_templ/p_example/ui_sidebar_right.R

@@ -23,7 +23,7 @@
 
 # -- Create Elements
 
-if (utils::packageVersion('shinydashboardPlus') < 2) {
+if (utils::packageVersion('shinydashboardPlus') < "2") {
     tab1 <- rightSidebarTabContent(
         id = 1,
         icon = "desktop",

inst/fw_templ/ui_plus.R

@@ -20,7 +20,7 @@ source(paste("program", "ui_body.R", sep = .Platform$file.sep),
 
 
 addl_opts <- list()
-if (utils::packageVersion('shinydashboardPlus') < 2) {
+if (utils::packageVersion('shinydashboardPlus') < "2") {
     plus_fxn  <- getExportedValue("shinydashboardPlus", "dashboardPagePlus")
     addl_opts <- list(sidebar_fullCollapse = TRUE)
 } else {

inst/fw_templ/ui_plus_no_sidebar.R

@@ -18,7 +18,7 @@ source(paste("program", "ui_body.R", sep = .Platform$file.sep),
 
 
 addl_opts <- list()
-if (utils::packageVersion('shinydashboardPlus') < 2) {
+if (utils::packageVersion('shinydashboardPlus') < "2") {
     plus_fxn  <- getExportedValue("shinydashboardPlus", "dashboardPagePlus")
     addl_opts <- list(sidebar_fullCollapse = TRUE)
 } else {

tests/testthat/_snaps/body_footer.md

@@ -6,7 +6,7 @@
           <h3 class="box-title">User Action Log</h3>
           <div class="box-tools pull-right">
             <button class="btn btn-box-tool" data-widget="collapse">
-              <i class="fa fa-plus" role="presentation" aria-label="plus icon"></i>
+              <i class="fas fa-plus" role="presentation" aria-label="plus icon"></i>
             </button>
           </div>
         </div>

tests/testthat/_snaps/download_file.md

@@ -2,7 +2,7 @@
 
     <span>
       <a id="myid-csv" class="btn btn-default shiny-download-link periscope-download-btn" href="" target="_blank" download>
-        <i class="fa fa-download" role="presentation" aria-label="download icon"></i>
+        <i class="fas fa-download" role="presentation" aria-label="download icon"></i>
       </a>
       <script>$(document).ready(function() {setTimeout(function() {shinyBS.addTooltip('myid-csv', 'tooltip', {'placement': 'top', 'trigger': 'hover', 'title': 'myhovertext'})}, 500)});</script>
     </span>
@@ -11,7 +11,7 @@
 
     <span class="btn-group">
       <button aria-expanded="false" aria-haspopup="true" class="btn btn-default action-button dropdown-toggle periscope-download-btn" data-toggle="dropdown" id="myid-downloadFileList" type="button">
-        <i class="fa fa-copy" role="presentation" aria-label="copy icon"></i>
+        <i class="far fa-copy" role="presentation" aria-label="copy icon"></i>
       </button>
       <ul class="dropdown-menu" id="myid-testList">
         <li>

tests/testthat/_snaps/downloadable_plot.md

@@ -1,13 +1,13 @@
 # downloadablePlotUI btn_overlap=true btn_halign=left btn_valign=bottom
 
     [[1]]
-    <div id="myid-dplotOutputID" class="shiny-plot-output" style="width:80%;height:300px;"></div>
+    <div class="shiny-plot-output html-fill-item" id="myid-dplotOutputID" style="width:80%;height:300px;"></div>
 
     [[2]]
     <span id="myid-dplotButtonDiv" class="periscope-downloadable-plot-button" style="display:none; padding: 5px;float:left;top: -50px">
       <span>
         <a id="myid-dplotButtonID-png" class="btn btn-default shiny-download-link periscope-download-btn" href="" target="_blank" download>
-          <i class="fa fa-download" role="presentation" aria-label="download icon"></i>
+          <i class="fas fa-download" role="presentation" aria-label="download icon"></i>
         </a>
         <script>$(document).ready(function() {setTimeout(function() {shinyBS.addTooltip('myid-dplotButtonID-png', 'tooltip', {'placement': 'top', 'trigger': 'hover', 'title': 'myhovertext'})}, 500)});</script>
       </span>
@@ -20,13 +20,13 @@
     <span id="myid-dplotButtonDiv" class="periscope-downloadable-plot-button" style="display:none; padding: 5px;float:none;margin-left:45%;top: -5px">
       <span>
         <a id="myid-dplotButtonID-png" class="btn btn-default shiny-download-link periscope-download-btn" href="" target="_blank" download>
-          <i class="fa fa-download" role="presentation" aria-label="download icon"></i>
+          <i class="fas fa-download" role="presentation" aria-label="download icon"></i>
         </a>
         <script>$(document).ready(function() {setTimeout(function() {shinyBS.addTooltip('myid-dplotButtonID-png', 'tooltip', {'placement': 'top', 'trigger': 'hover', 'title': 'myhovertext'})}, 500)});</script>
       </span>
     </span>
 
     [[2]]
-    <div id="myid-dplotOutputID" class="shiny-plot-output" style="width:80%;height:300px;"></div>
+    <div class="shiny-plot-output html-fill-item" id="myid-dplotOutputID" style="width:80%;height:300px;"></div>
 
 

tests/testthat/_snaps/downloadable_table.md

@@ -4,14 +4,14 @@
     <span id="myid-dtableButtonDiv" class="periscope-downloadable-table-button" style="">
       <span>
         <a id="myid-dtableButtonID-csv" class="btn btn-default shiny-download-link periscope-download-btn" href="" target="_blank" download>
-          <i class="fa fa-download" role="presentation" aria-label="download icon"></i>
+          <i class="fas fa-download" role="presentation" aria-label="download icon"></i>
         </a>
         <script>$(document).ready(function() {setTimeout(function() {shinyBS.addTooltip('myid-dtableButtonID-csv', 'tooltip', {'placement': 'top', 'trigger': 'hover', 'title': 'myHoverText'})}, 500)});</script>
       </span>
     </span>
 
     [[2]]
-    <div id="myid-dtableOutputID" style="width:100%; height:auto; " class="datatables html-widget html-widget-output"></div>
+    <div class="datatables html-widget html-widget-output shiny-report-size html-fill-item-overflow-hidden html-fill-item" id="myid-dtableOutputID" style="width:100%;height:auto;"></div>
 
     [[3]]
     <input id="myid-dtableOutputHeight" type="text" class="shiny-input-container hidden" value="200px"/>

tests/testthat/_snaps/ui_functions.md

@@ -9,7 +9,7 @@
       </span>
       <nav class="navbar navbar-static-top" role="navigation">
         <span style="display:none;">
-          <i class="fa fa-bars" role="presentation" aria-label="bars icon"></i>
+          <i class="fas fa-bars" role="presentation" aria-label="bars icon"></i>
         </span>
         <a href="#" class="sidebar-toggle" data-toggle="offcanvas" role="button">
           <span class="sr-only">Toggle navigation</span>
@@ -106,7 +106,7 @@
               <h3 class="box-title">User Action Log</h3>
               <div class="box-tools pull-right">
                 <button class="btn btn-box-tool" data-widget="collapse">
-                  <i class="fa fa-plus" role="presentation" aria-label="plus icon"></i>
+                  <i class="fas fa-plus" role="presentation" aria-label="plus icon"></i>
                 </button>
               </div>
             </div>
@@ -159,7 +159,7 @@
       </span>
       <nav class="navbar navbar-static-top" role="navigation">
         <span style="display:none;">
-          <i class="fa fa-bars" role="presentation" aria-label="bars icon"></i>
+          <i class="fas fa-bars" role="presentation" aria-label="bars icon"></i>
         </span>
         <a href="#" class="sidebar-toggle" data-toggle="offcanvas" role="button">
           <span class="sr-only">Toggle navigation</span>
@@ -171,7 +171,7 @@
           <ul class="nav navbar-nav">
             <li>
               <a href="#" data-toggle="control-sidebar">
-                <i class="fa fa-cogs" role="presentation" aria-label="cogs icon"></i>
+                <i class="fas fa-gears" role="presentation" aria-label="gears icon"></i>
               </a>
             </li>
           </ul>

tests/testthat/sample_app_both_sidebar/program/ui_sidebar_right.R

@@ -23,7 +23,7 @@
 
 # -- Create Elements
 
-if (utils::packageVersion('shinydashboardPlus') < 2) {
+if (utils::packageVersion('shinydashboardPlus') < "2") {
     tab1 <- rightSidebarTabContent(
         id = 1,
         icon = "desktop",

tests/testthat/sample_app_both_sidebar/ui.R

@@ -20,7 +20,7 @@ source(paste("program", "ui_body.R", sep = .Platform$file.sep),
 
 
 addl_opts <- list()
-if (utils::packageVersion('shinydashboardPlus') < 2) {
+if (utils::packageVersion('shinydashboardPlus') < "2") {
     plus_fxn  <- getExportedValue("shinydashboardPlus", "dashboardPagePlus")
     addl_opts <- list(sidebar_fullCollapse = TRUE)
 } else {

tests/testthat/sample_app_r_sidebar/program/ui_sidebar_right.R

@@ -23,7 +23,7 @@
 
 # -- Create Elements
 
-if (utils::packageVersion('shinydashboardPlus') < 2) {
+if (utils::packageVersion('shinydashboardPlus') < "2") {
     tab1 <- rightSidebarTabContent(
         id = 1,
         icon = "desktop",

tests/testthat/sample_app_r_sidebar/ui.R

@@ -18,7 +18,7 @@ source(paste("program", "ui_body.R", sep = .Platform$file.sep),
 
 
 addl_opts <- list()
-if (utils::packageVersion('shinydashboardPlus') < 2) {
+if (utils::packageVersion('shinydashboardPlus') < "2") {
     plus_fxn  <- getExportedValue("shinydashboardPlus", "dashboardPagePlus")
     addl_opts <- list(sidebar_fullCollapse = TRUE)
 } else {

tests/testthat/setup.R

@@ -13,4 +13,4 @@ if (interactive()) {
 }
 
 # indicator for shinydashboardPlus version
-t_sdp_old <- utils::packageVersion('shinydashboardPlus') < 2.0
+t_sdp_old <- utils::packageVersion('shinydashboardPlus') < "2"