Merge pull request #26 from HendrikSchultheis/cran_request

testthat package

.buildkite/pipeline.yml

@@ -5,7 +5,8 @@ steps:
       - ". /etc/profile.d/conda.sh"
       - "conda activate wilson"
 #      - "Rscript -e 'install.packages(\"rje\")'"
-      - "Rscript -e 'devtools::check()'"
+      - "R CMD build ."
+      - "R CMD check *tar.gz --as-cran"
 
 #  - wait
 

.buildkite/wilson-env.yml

@@ -16,7 +16,7 @@ dependencies:
   - r-RColorBrewer
   - r-shinyjs
   - r-viridis
-#  - r-rje
+  - r-rje
 #  - r-grdevices # base package
 #  - r-grid # base package
   - r-plyr
@@ -43,3 +43,6 @@ dependencies:
   - r-devtools
   - "readline==6.3"
   - r-roxygen2
+  - r-rmarkdown
+  - r-testthat
+#  - r-vdiffr # not yet in conda-forge

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: wilson
 Type: Package
 Title: Web-Based Interactive Omics Visualization
-Version: 2.0.0
+Version: 2.0.1
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),
@@ -50,5 +50,6 @@ RoxygenNote: 6.0.1
 biocViews: 
 Suggests: knitr,
     rmarkdown,
-    testthat
+    testthat,
+    vdiffr
 VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,5 @@
+# wilson 2.0.1
+- tests added
 # wilson 2.0.0 
 ## Features
 - clarion class:

R/function.R

@@ -125,7 +125,7 @@ create_scatterplot <- function(data, data.labels = NULL, data.hovertext = NULL,
   if (density) {
     ### kernel density
     # plot$layers <- c(stat_density2d(geom = "tile", aes(fill = ..density..^0.25), n=200, contour=FALSE) + aes_(fill = as.name(var)), plot$layers) # n = resolution; density less sparse
-    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes_(fill = ~ ..density.. ^ 0.25), n = 200, contour = FALSE)
+    plot <- plot + ggplot2::stat_density2d(geom = "tile", ggplot2::aes_(fill = ~ ..density.. ^ 0.25, color = NULL), n = 200, contour = FALSE)
 
     plot <- plot + ggplot2::scale_fill_gradient(low = "white", high = "black") +
       # guides(fill=FALSE) +		# remove density legend
@@ -1152,7 +1152,7 @@ searchData <- function(input, choices, options = c("=", "<", ">"), min. = min(ch
       }
 
       # range
-      if ("inner" == options){
+      if ("inner" == options) {
         if (x >= input[1] & x <= input[2]) return(TRUE)
       }
       if ("outer" == options) {
@@ -1203,15 +1203,17 @@ searchData <- function(input, choices, options = c("=", "<", ">"), min. = min(ch
 download <- function(file, filename, plot, width, height, ppi = 72, save_plot = TRUE, ui = NULL) {
   session <- shiny::getDefaultReactiveDomain()
 
-  # show notification
-  shiny::showNotification(
-    id = session$ns("download-note"),
-    shiny::tags$b("Preparing download files. Please wait..."),
-    duration = NULL,
-    closeButton = FALSE,
-    type = "message"
-  )
-  shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("download-note")), "')).addClass('notification-position-center');"))
+  if (!is.null(session)) {
+    # show notification
+    shiny::showNotification(
+      id = session$ns("download-note"),
+      shiny::tags$b("Preparing download files. Please wait..."),
+      duration = NULL,
+      closeButton = FALSE,
+      type = "message"
+    )
+    shinyjs::runjs(paste0("$(document.getElementById('", paste0("shiny-notification-", session$ns("download-note")), "')).addClass('notification-position-center');"))
+  }
 
   # cut off file extension
   name <- sub("(.*)\\..*$", replacement = "\\1", filename)
@@ -1283,8 +1285,10 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
   # remove tmp files
   file.remove(files)
 
-  # remove notification
-  shiny::removeNotification(session$ns("download-note"))
+  if (!is.null(session)) {
+    # remove notification
+    shiny::removeNotification(session$ns("download-note"))
+  }
 
   return(out)
 }

R/global.R

@@ -11,8 +11,10 @@ wilson.globals <- new.env(parent = emptyenv())
 #'
 #' @export
 set_logger <- function(logger, token = NULL) {
-  if (is.null(logger) || methods::is(logger, "logger")) {
+  if (methods::is(logger, "logger")) {
     assign(x = paste0("logger", token), value = logger, envir = wilson.globals)
+  } else if (is.null(logger)) {
+    rm(list = paste0("logger", token), envir = wilson.globals)
   }
 }
 

cran-comments.md

@@ -1,3 +1,4 @@
+# Submission 1
 ## Test environments
 * local windows 7 install, R 3.5.1
 * debian 9.4, R 3.4.1
@@ -20,3 +21,37 @@ There was 1 NOTE:
 I have also run R CMD check on downstream dependencies of wilson 
 (https://github.molgen.mpg.de/loosolab/wilson/tree/master/revdep). 
 All packages that I could install passed.
+
+## Reviewer comments
+Thanks, we see you have lots of cuntions without examples (which may be reasonable given they are not intended t be called by users directly). 
+Nevertheless, it would be good to have them tested, so please create, if examples are not feasible, at least tests that execute the various functions in your package.
+
+Best,
+Uwe Ligges
+
+# Submission 2
+## Test environments
+* local windows 7 install, R 3.5.1
+* debian 9.4, R 3.4.1
+* win-builder (devel and release)
+
+## Submission comments
+Addressed reviewer comments by adding tests where possible.
+
+## R CMD check results
+There were no ERRORs or WARNINGs.
+
+There was 1 NOTE:
+
+* New submission
+
+* Possibly mis-spelled words in DESCRIPTION:
+  Omics (3:30)
+  omics (9:126)
+
+  Both are spelled correctly. First is capital because of title case.
+
+## Downstream dependencies
+I have also run R CMD check on downstream dependencies of wilson 
+(https://github.molgen.mpg.de/loosolab/wilson/tree/master/revdep). 
+All packages that I could install passed.

revdep/README.md

@@ -10,7 +10,7 @@
 |language |(EN)                         |
 |collate  |German_Germany.1252          |
 |tz       |Europe/Berlin                |
-|date     |2018-07-04                   |
+|date     |2018-07-16                   |
 
 ## Packages
 
@@ -24,10 +24,10 @@
 |DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.1)                      |
 |factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.1)                      |
 |FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.1)                      |
-|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.1)                      |
+|ggplot2         |   |3.0.0   |2018-07-03 |CRAN (R 3.5.1)                      |
 |ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.1)                      |
 |gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.1)                      |
-|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.1)                      |
+|heatmaply       |   |0.15.2  |2018-07-06 |CRAN (R 3.5.1)                      |
 |knitr           |   |1.20    |2018-02-20 |CRAN (R 3.5.1)                      |
 |log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.1)                      |
 |openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.1)                      |
@@ -46,8 +46,10 @@
 |shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.1)                      |
 |shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.1)                      |
 |shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.1)                      |
+|testthat        |   |2.0.0   |2017-12-13 |CRAN (R 3.5.1)                      |
+|vdiffr          |   |0.2.3   |2018-04-27 |CRAN (R 3.5.1)                      |
 |viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.1)                      |
-|wilson          |*  |2.0.0   |2018-07-04 |local (HendrikSchultheis/wilson@NA) |
+|wilson          |   |2.0.1   |2018-07-16 |local (HendrikSchultheis/wilson@NA) |
 
 # Check results
 

revdep/problems.md

@@ -10,7 +10,7 @@
 |language |(EN)                         |
 |collate  |German_Germany.1252          |
 |tz       |Europe/Berlin                |
-|date     |2018-07-04                   |
+|date     |2018-07-16                   |
 
 ## Packages
 
@@ -24,10 +24,10 @@
 |DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.1)                      |
 |factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.1)                      |
 |FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.1)                      |
-|ggplot2         |   |2.2.1   |2016-12-30 |CRAN (R 3.5.1)                      |
+|ggplot2         |   |3.0.0   |2018-07-03 |CRAN (R 3.5.1)                      |
 |ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.1)                      |
 |gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.1)                      |
-|heatmaply       |   |0.15.0  |2018-06-23 |CRAN (R 3.5.1)                      |
+|heatmaply       |   |0.15.2  |2018-07-06 |CRAN (R 3.5.1)                      |
 |knitr           |   |1.20    |2018-02-20 |CRAN (R 3.5.1)                      |
 |log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.1)                      |
 |openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.1)                      |
@@ -46,8 +46,10 @@
 |shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.1)                      |
 |shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.1)                      |
 |shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.1)                      |
+|testthat        |   |2.0.0   |2017-12-13 |CRAN (R 3.5.1)                      |
+|vdiffr          |   |0.2.3   |2018-04-27 |CRAN (R 3.5.1)                      |
 |viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.1)                      |
-|wilson          |*  |2.0.0   |2018-07-04 |local (HendrikSchultheis/wilson@NA) |
+|wilson          |   |2.0.1   |2018-07-16 |local (HendrikSchultheis/wilson@NA) |
 
 # Check results