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Handle Bioconductor packages via devtools #49

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Merged
ressy merged 3 commits into from
Jul 19, 2019
Merged

Handle Bioconductor packages via devtools #49

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fb170b8
Try handling bioconductor installs via devtools
ressy Jul 17, 2019
4cc5afa
Remove msa reference in Travis config
ressy Jul 18, 2019
d83f94a
more stringent error handling in install scripts
ressy Jul 18, 2019
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1 change: 0 additions & 1 deletion .travis.yml
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Expand Up @@ -4,7 +4,6 @@ os:
- osx
# https://docs.travis-ci.com/user/languages/r
language: r
bioc_packages: msa
r:
- oldrel
- release
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -8,6 +8,7 @@ License: file LICENSE
Encoding: UTF-8
LazyData: true
Language: en-US
biocViews:
Imports:
argparser (>= 0.4),
Biostrings (>= 2.38.4),
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8 changes: 0 additions & 8 deletions R/installer.R
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Expand Up @@ -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")
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2 changes: 2 additions & 0 deletions install_linux.sh
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Expand Up @@ -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"
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2 changes: 2 additions & 0 deletions install_mac.command
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Expand Up @@ -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"
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