From fb170b85e8959633bac24490560de43d86b89894 Mon Sep 17 00:00:00 2001
From: Jesse Connell <ancon@upenn.edu>
Date: Wed, 17 Jul 2019 17:51:20 -0400
Subject: [PATCH 1/3] Try handling bioconductor installs via devtools

I hear devtools can magically install packages from bioconductor.  Let's
try it.
https://bioinformatics.stackexchange.com/a/3375
---
 DESCRIPTION   | 1 +
 R/installer.R | 8 --------
 2 files changed, 1 insertion(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a3b9073..0cad7ed 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,6 +8,7 @@ License: file LICENSE
 Encoding: UTF-8
 LazyData: true
 Language: en-US
+biocViews:
 Imports:
   argparser (>= 0.4),
   Biostrings (>= 2.38.4),
diff --git a/R/installer.R b/R/installer.R
index f698fd2..4f54837 100644
--- a/R/installer.R
+++ b/R/installer.R
@@ -168,14 +168,6 @@ install <- function(path_package) {
     install.packages("devtools", repos = "https://cloud.r-project.org")
   }
 
-  if (! haspkg("msa")) {
-    cat("\n")
-    cat("### Installing Bioconductor and MSA\n")
-    cat("\n")
-    source("https://bioconductor.org/biocLite.R")
-    biocLite("msa", suppressUpdates = TRUE)
-  }
-
   cat("\n")
   cat("### Installing CHIIMP\n")
   cat("\n")

From 4cc5afa0a86e88d2c59bbda804774dc3808432bc Mon Sep 17 00:00:00 2001
From: Jesse Connell <ancon@upenn.edu>
Date: Thu, 18 Jul 2019 10:30:53 -0400
Subject: [PATCH 2/3] Remove msa reference in Travis config

If devtools is really supplying msa, we don't need Travis to think about
it.
---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index cab5f6a..7524ab5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,7 +4,6 @@ os:
   - osx
 # https://docs.travis-ci.com/user/languages/r
 language: r
-bioc_packages: msa
 r:
   - oldrel
   - release

From d83f94acaa72eaf4903a818b83f6d7d2ea30380a Mon Sep 17 00:00:00 2001
From: Jesse Connell <ancon@upenn.edu>
Date: Thu, 18 Jul 2019 16:34:25 -0400
Subject: [PATCH 3/3] more stringent error handling in install scripts

---
 install_linux.sh    | 2 ++
 install_mac.command | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/install_linux.sh b/install_linux.sh
index 0e8f4b3..879d9c6 100755
--- a/install_linux.sh
+++ b/install_linux.sh
@@ -5,6 +5,8 @@
 # A base R install is assumed to already be present, but all dependencies
 # should be installed automatically here.
 
+set -e
+
 rscript=$(which Rscript)
 pkgdir=$(readlink -f $(dirname $BASH_SOURCE))
 cd "$pkgdir"
diff --git a/install_mac.command b/install_mac.command
index 5ba5761..878e81b 100755
--- a/install_mac.command
+++ b/install_mac.command
@@ -5,6 +5,8 @@
 # A base R install is assumed to already be present, but all dependencies
 # should be installed automatically here.
 
+set -e
+
 rscript=$(which Rscript)
 pkgdir=$(dirname $BASH_SOURCE)
 cd "$pkgdir"