Commit 4da4b6e5 authored by Holger Brandl's avatar Holger Brandl

renamed .inst_pack to install_package

parent d9e464cd
......@@ -5,7 +5,7 @@
#loadpack(Biostrings)
## install Biostrings if not yet there
.inst_pack("Biostrings")
install_package("Biostrings")
read.fasta <- function(fileName){
......@@ -40,7 +40,7 @@ write_fasta <- function(seq_names, sequences, file){
}
getSeqLengthFromFasta <- function(fileName){
get_sequence_lengths <- function(fileName){
assembly <- mutate(read_fasta(fileName), seq_len=nchar(Sequence))
assembly$Sequence = NULL
return(assembly)
......@@ -67,10 +67,6 @@ write_bed <- function(bedData, file){
options(scipen=oldScipen)
}
write.bed <- function(bedData, file){
warning("Deprecated: use write_bed instead!")
write_bed(bedData, file)
}
## reload to fix rename overloading
#reload_dplyr()
......@@ -53,7 +53,7 @@ require_auto <- function(x){
}
## externalized installer to also allow for installation without loading
.inst_pack <- function(x){
install_package <- function(x){
if(!isTRUE(x %in% .packages(all.available=TRUE)) && any(available.packages()[,1]==x)) {
# update.packages(ask=F) # update dependencies, if any.
eval(parse(text=paste("install.packages('", x, "')", sep="")))
......@@ -73,7 +73,7 @@ require_auto <- function(x){
load_pack <- function(x, warn_conflicts=T){
x <- as.character(substitute(x));
.inst_pack(x)
install_package(x)
## load it using a library function so that loadpack errors if package is still not ins
eval(parse(text=paste("library(", x, ", quietly=T, warn.conflicts=", warn_conflicts, ")", sep="")))
......@@ -84,7 +84,7 @@ loadpack <- function(x, warn_conflicts=T){
x <- as.character(substitute(x));
.inst_pack(x)
install_package(x)
## load it using a library function so that loadpack errors if package is still not ins
eval(parse(text=paste("library(", x, ", quietly=T, warn.conflicts=", warn_conflicts, ")", sep="")))
......
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