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 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") 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"