Merge 42ebce8 into c32c7c3

.Rbuildignore

@@ -15,12 +15,6 @@ Makefile
 inst/shiny/rsconnect
 
 # Generated files in inst/shiny/www/..
-inst/shiny/*
-inst/shiny/www/report_full.Rmd
-inst/shiny/www/report_full.html
-inst/shiny/www/report_full_purl.R
-inst/shiny/www/report_meta.Rmd
-inst/shiny/www/report_meta.html
-inst/shiny/www/report_meta_purl.R
+inst/shiny/www/report_expanded.*
 data/freshVsFrozen.csv
 data/u133VsExon.csv

.travis.yml

@@ -16,7 +16,13 @@ r_github_packages:
 after_success:
   - Rscript -e 'covr::coveralls()'
 
+after_failure:
+  - Rscript -e 'sessionInfo()'
+  - Rscript -e 'installed.packages()'
+
 notifications:
   email:
     on_success: change
     on_failure: change
+
+

DESCRIPTION

@@ -24,6 +24,7 @@ Suggests:
     rmarkdown,
     shiny,
     shinydashboard,
+    shinyBS,
     rhandsontable,
     DT
 VignetteBuilder: knitr

GMCM.Rproj

@@ -18,7 +18,7 @@ StripTrailingWhitespace: Yes
 
 BuildType: Package
 PackageInstallArgs: --resave-data
-PackageBuildArgs: --resave-data --compact-vignettes=both
+PackageBuildArgs: --resave-data --compact-vignettes=both --with-keep.source
 PackageBuildBinaryArgs: --resave-data
 PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,namespace

NAMESPACE

@@ -39,4 +39,5 @@ importFrom(stats,rchisq)
 importFrom(stats,rnorm)
 importFrom(stats,runif)
 importFrom(utils,flush.console)
+importFrom(utils,write.csv2)
 useDynLib(GMCM)

R/cput.R

@@ -0,0 +1,7 @@
+# dput object to character string
+# cput is used inside the reports
+cput <- function(x) {
+  f <- tempfile()
+  dput(x, file = f)
+  return(readLines(f))
+}

R/run_full_report.R

@@ -0,0 +1,51 @@
+#' @importFrom utils write.csv2
+run_full_report <- function(...) {
+
+  # Simulate some data and put it into a CSV file
+  sim_data <- SimulateGMCMData(n = 1000, par = c(pie1 = 0.3, mu = 2,
+                                                 sigma = 1.1, rho = 0.2))$z
+  colnames(sim_data) <- c("u133", "exon")
+  data_file <- tempfile()
+  utils::write.csv2(sim_data, file = data_file)
+
+
+  # SPECIAL GMCM ----
+  report_path_meta <- system.file("shiny", "www", "report_meta.Rmd",
+                                  package = "GMCM", lib.loc = .libPaths()[1],
+                                  mustWork = TRUE)
+
+  # Parameters to expand
+  params <- list(data_file = data_file,
+                 header = TRUE,
+                 sep = ";",
+                 quote = '\"',
+                 model_cols = c("u133", "exon"),
+                 meta_large_vals = FALSE,
+                 init_par = c(pie1 = 0.5, mu = 1, sigma = 1, rho = 0.5),
+                 meta_method = "NM",
+                 meta_max_ite = 50,
+                 meta_positive_rho = TRUE,
+                 meta_IDR_thres_type = "IDR",
+                 meta_IDR_thres = 0.01)
+
+  expand_args <- c(list(file = report_path_meta), params)
+  report_expanded <- do.call(knitr::knit_expand, expand_args)
+
+  # Write to file
+  report_expanded_path <- tempfile()
+  cat(report_expanded, file = report_expanded_path)
+
+  # We can also purl
+  res1 <- knitr::purl(report_expanded_path,
+                      output = gsub(".Rmd$", ".R", report_expanded_path),
+                      documentation = 0)
+
+  # Render the expanded document
+  res2 <- rmarkdown::render(
+    input = report_expanded_path,
+    output_options = list(self_contained = TRUE),
+    envir = new.env(parent = globalenv())
+  )
+
+  return(invisible(list(report_expanded_path, res1, res2)))
+}

R/run_meta_report.R

@@ -0,0 +1,49 @@
+#' @importFrom utils write.csv2
+run_meta_report <- function(...) {
+
+  # Simulate some data and put it into a CSV file
+  sim_data <- SimulateGMCMData(n = 1000, par = c(pie1 = 0.3, mu = 2,
+                                                 sigma = 1.1, rho = 0.2))$z
+  colnames(sim_data) <- c("u133", "exon")
+  data_file <- tempfile()
+  utils::write.csv2(sim_data, file = data_file)
+
+
+  # GENERAL GMCM ----
+  report_path_full <- system.file("shiny", "www", "report_full.Rmd",
+                                  package = "GMCM", lib.loc = .libPaths()[1],
+                                  mustWork = TRUE)
+
+  # Parameters to expand
+  params <- list(data_file = data_file,
+                 header = TRUE,
+                 sep = ";",
+                 quote = '\"',
+                 model_cols = c("u133", "exon"),
+                 theta = GMCM::rtheta(m = 2, d = 2),
+                 fit_method = "NM",
+                 max_ite = 50,
+                 full_class_type = "thres_prob",
+                 full_thres_prob = 0.9)
+
+  expand_args <- c(list(file = report_path_full), params)
+  report_expanded <- do.call(knitr::knit_expand, expand_args)
+
+  # Write to temp file
+  report_expanded_path <- tempfile()
+  cat(report_expanded, file = report_expanded_path)
+
+  # We can purl
+  res3 <- knitr::purl(report_expanded_path,
+                      output = paste0(report_expanded_path, ".R"),
+                      documentation = 0)
+
+  # Render the expanded document
+  res4 <- rmarkdown::render(
+    input = report_expanded_path,
+    output_options = list(self_contained = TRUE),
+    envir = new.env(parent = globalenv())
+  )
+
+  return(invisible(list(report_expanded_path, res3, res4)))
+}

tests/testthat/test-shiny-reports.R

@@ -4,12 +4,8 @@ test_that("shiny reports can be expanded and rendered", {
   skip_on_cran()
 
   # Expect no errors (i.e. fail to provide errors)
-  expect_error(
-    capture_messages(capture_output( # Make render shut up
-      source(system.file("shiny/run-reports.R", package = "GMCM"))
-    )),
-    NA
-  )
+  expect_error(GMCM:::run_meta_report(), NA)
+  expect_error(GMCM:::run_full_report(), NA)
 })