Adaptation of run() to install latest release matching the svbox version

Author: phgrosjean

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioDataScience
 Type: Package
-Version: 0.25.0
+Version: 2018.0.0
 Title: A Series of Learnr Documents for Biological Data Science
 Description: Interactive documents using learnr for studying biological data science.
 Authors@R: c(

NEWS.md

@@ -1,57 +1,75 @@
 # BioDataScience News
 
+## Changes in version 2018.0.0
+
+- `run()` modified to install latest release matching svbox year.
+
+
 ## Changes in version 0.25.0
 
-- Review of the all tutoriels (00a - 13c) with the **svbox 2018**
+- Review of the all tutorials (00a - 13c) with the **svbox 2018**
 
 ## Changes in version 0.24.0
 
 - Tutorial examen_c finalized
 
+
 ## Changes in version 0.23.1
 
 - Review tutorials 00 and 02 with svbox2019
 
+
 ## Changes in version 0.23.0
 
 - Review of the all tutoriels (02a - 12a)
 
+
 ## Changes in version 0.22.0
 
 - Tutorial examen_b finalized
 
+
 ## Changes in version 0.21.0
 
 - Tutorial examen_a finalized
 
+
 ## Changes in version 0.20.0
 
 - Tutorial 12a_correlation finalized
 
+
 ## Changes in version 0.19.0
 
-- correction of bug to 11b and 11a
+- Correction of bugs to 11b and 11a
+
 
 ## Changes in version 0.18.2
 
 - Tutorial 11b_syntaxr finalized
+
 - Tutorial 11a_anova2 finalized
 
+
 ## Changes in version 0.18.0
 
 - Tutorial 11b_syntaxr finalized
 
+
 ## Changes in version 0.17.0
 
 - Tutorial 11a_anova2 finalized
 
+
 ## Changes in version 0.16.0
 
 - Tutorial 10b_anova finalized
 
+
 ## Changes in version 0.15.0
 
 - Tutorial 10a_anova finalized
+
 - Addition of a test shiny app (histogram.R)
 
 
@@ -64,33 +82,41 @@
 
 - Tutorial 09a_student finalized
 
+
 ## Changes in version 0.12.1
 
 - Tutorial 08b_chi2 finalized
-- add html file 08b_chi2
+
+- Add html file 08b_chi2
+
 
 ## Changes in version 0.12.0
 
 - Tutorial 08b_chi2 finalized
 
+
 ## Changes in version 0.11.0
 
 - Tutorial 08a_chi2 finalized
 
+
 ## Changes in version 0.10.0
 
 - Tutorial 07b_distri finalized
 
+
 ## Changes in version 0.9.0
 
 - Tutorial 07a_proba finalized
+
 - Tutorial 06a_test finalized
 
 
 ## Changes in version 0.8.0
 
 - Tutorial 05a_test finalized
 
+
 ## Changes in version 0.7.0
 
 - Tutorial 04a_test finalized

R/run.R

@@ -86,18 +86,50 @@ run <- function(tutorial, ..., update = ask, ask = interactive()) {
     github_response(req)
   }
 
+  get_last_tag <- function() {
+    # Check if run from within a SciViews Box
+    hostname <- ""
+    if (file.exists("/etc/hostname"))
+      hostname <- readLines("/etc/hostname")[1]
+    if (!grepl("^box[0-9]{4}", hostname))
+      warning(paste("Not run from withing a SciViews Box:",
+        "no update and expect weird behavior of the tutorials"))
+
+    # Get the year of the SciViews Box
+    box_year <- substr(hostname, 4, 7)
+    # Pattern is v[box_year].x.y
+    v_pat <- paste0("^[vV]", box_year, "\\.[0-9]+\\.[0-9]+$")
+
+    # Get all tags for BioDataScience
+    good_tags <- character(0)
+    all_tags_data <- try(github_GET(
+      "repos/BioDataScience-Course/BioDataScience/releases"),
+      silent = TRUE)
+    if (!inherits(all_tags_data, "try-error")) {
+      all_tags <- sapply(all_tags_data, getElement, "tag_name")
+      # Keep only tags related to this svbox
+      good_tags <- all_tags[grepl(v_pat, all_tags)]
+    }
+    # Return latest (first one) among all valid tags
+    if (length(good_tags)) good_tags[1] else NULL
+  }
+
   # Look what is latest release and compare with current version of the package
   updated <- FALSE
   if (isTRUE(update)) {
-    last_tag <- try(github_GET(
-      "repos/BioDataScience-Course/BioDataScience/releases/latest")$tag_name,
-      silent = TRUE)
-    if (!inherits(last_tag, "try-error") &&
-        grepl("^[vV][0-9]+\\.[0-9]+\\.[0-9]+$", last_tag)) {
+    #last_tag <- try(github_GET(
+    #  "repos/BioDataScience-Course/BioDataScience/releases/latest")$tag_name,
+    #  silent = TRUE)
+    #if (!inherits(last_tag, "try-error") &&
+    #    grepl("^[vV][0-9]+\\.[0-9]+\\.[0-9]+$", last_tag)) {
+    last_tag <- get_last_tag()
+    if (!is.null(last_tag)) {
       last_rel <- sub("^[vV]([0-9]+\\.[0-9]+)\\.([0-9]+)$", "\\1-\\2", last_tag)
       curr_rel <- sub("^([0-9]+\\.[0-9]+)\\.([0-9]+)$", "\\1-\\2",
         packageVersion("BioDataScience"))
-      status <- try(compareVersion(last_rel, curr_rel) > 0, silent = TRUE)
+      # In previous version we tested if compareVersion() > 0, but here, we
+      # rather check if it is different, cf. may need to downgrade possibly
+      status <- try(compareVersion(last_rel, curr_rel) != 0, silent = TRUE)
       if (!inherits(status, "try-error")) {
         if (status > 0) {
           # We need to update the package