From bca40d8b58ea01ecebb5dcbddcf572cd25c5ce8e Mon Sep 17 00:00:00 2001
From: Jesse Connell <ancon@upenn.edu>
Date: Thu, 14 Mar 2019 09:46:17 -0400
Subject: [PATCH 1/4] Add "pause" statement to Windows installer

This makes it easier to see the installation outcome.  (Otherwise the
cmd.exe window closes as soon as the installer finishes.)
---
 install_windows.cmd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/install_windows.cmd b/install_windows.cmd
index 3441b26..4517fd3 100755
--- a/install_windows.cmd
+++ b/install_windows.cmd
@@ -17,3 +17,4 @@ set pkgdir=%~dp0
 
 REM  Run bulk of the install within R.
 "%rscript%" --vanilla "%pkgdir%\install_windows.R"
+pause

From cb3f371495452ebdbc2eac5e349ad562264f2b20 Mon Sep 17 00:00:00 2001
From: Jesse Connell <ancon@upenn.edu>
Date: Thu, 14 Mar 2019 09:47:28 -0400
Subject: [PATCH 2/4] Simplify Windows install; do not auto-update deps

Only install devtools and msa if not already present; do not run
separate dependency install and package test steps as they're already
handled in devtools::install(); Disable devtools' automatic package
upgrades during install.
---
 install_windows.R | 33 ++++++++++-----------------------
 1 file changed, 10 insertions(+), 23 deletions(-)

diff --git a/install_windows.R b/install_windows.R
index f9fef14..07cc54f 100755
--- a/install_windows.R
+++ b/install_windows.R
@@ -21,38 +21,25 @@ if (! any(file.access(.libPaths(), 2) == 0)) {
   .libPaths(dp)
 }
 
-cat("\n")
-cat("### Installing devtools\n")
-cat("\n")
-install.packages("devtools", repos = "https://cloud.r-project.org")
-
-cat("\n")
-cat("### Installing Bioconductor and MSA\n")
-cat("\n")
-source("https://bioconductor.org/biocLite.R")
-biocLite("msa")
-
-cat("\n")
-cat("### Installing dependencies\n")
-cat("\n")
-devtools::install_deps(path, dependencies = TRUE)
-
-cat("\n")
-cat("### Testing CHIIMP\n")
-cat("\n")
-status <- sum(as.data.frame(devtools::test(path))$failed)
-if (status == 1) {
+if (! require("devtools", character.only = TRUE, quietly = TRUE)) {
   cat("\n")
+  cat("### Installing devtools\n")
   cat("\n")
-  cat("    Warning: Tests indicated failures.\n")
+  install.packages("devtools", repos = "https://cloud.r-project.org")
+}
+
+if (! suppressMessages(require("msa", character.only = TRUE, quietly = TRUE))) {
   cat("\n")
+  cat("### Installing Bioconductor and MSA\n")
   cat("\n")
+  source("https://bioconductor.org/biocLite.R")
+  biocLite("msa")
 }
 
 cat("\n")
 cat("### Installing CHIIMP\n")
 cat("\n")
-devtools::install(path)
+devtools::install(path, upgrade = "never")
 
 shortcut_path <- file.path(UPROF, "Desktop", "CHIIMP.lnk")
 chiimp_path <- system.file("bin", "chiimp.cmd", package = "chiimp")

From 349222b116a32719c80b3cc96bca45c0c363f25c Mon Sep 17 00:00:00 2001
From: Jesse Connell <ancon@upenn.edu>
Date: Thu, 14 Mar 2019 10:19:34 -0400
Subject: [PATCH 3/4] quieter package checks for windows installer

---
 install_windows.R | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/install_windows.R b/install_windows.R
index 07cc54f..b0e9103 100755
--- a/install_windows.R
+++ b/install_windows.R
@@ -21,14 +21,20 @@ if (! any(file.access(.libPaths(), 2) == 0)) {
   .libPaths(dp)
 }
 
-if (! require("devtools", character.only = TRUE, quietly = TRUE)) {
+haspkg <- function(pkgname) {
+  suppressMessages(suppressWarnings(
+    require(pkgname, character.only = TRUE, quietly = TRUE)
+  ))
+}
+
+if (! haspkg("devtools")) {
   cat("\n")
   cat("### Installing devtools\n")
   cat("\n")
   install.packages("devtools", repos = "https://cloud.r-project.org")
 }
 
-if (! suppressMessages(require("msa", character.only = TRUE, quietly = TRUE))) {
+if (! haspkg("msa")) {
   cat("\n")
   cat("### Installing Bioconductor and MSA\n")
   cat("\n")

From f4a904a6c85714ca129038843476a68b0bddeee0 Mon Sep 17 00:00:00 2001
From: Jesse Connell <ancon@upenn.edu>
Date: Thu, 14 Mar 2019 10:27:25 -0400
Subject: [PATCH 4/4] Also do not auto-update deps for msa package

---
 install_windows.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_windows.R b/install_windows.R
index b0e9103..1d22178 100755
--- a/install_windows.R
+++ b/install_windows.R
@@ -39,7 +39,7 @@ if (! haspkg("msa")) {
   cat("### Installing Bioconductor and MSA\n")
   cat("\n")
   source("https://bioconductor.org/biocLite.R")
-  biocLite("msa")
+  biocLite("msa", suppressUpdates = TRUE)
 }
 
 cat("\n")