check.binary: checks if binary is in the path

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Description

check if a binary is in the path. Specifically used for bedtools, bedops and tabix.

Usage

check.binary(x = "bedtools", verbose = TRUE)

Arguments

x	a string referring to a binary/executable i.e. bedtools, bedops, tabix
verbose	print log

Details

Used internally to determine functionality selection options.

Value

TRUE or FALSE

Author(s)

Daryl Waggott

Examples

check.binary("bedtools")

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied


######################
#### bedr v1.0.3 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

  * Checking path for bedtools... sh: 1: cannot create /dev/null: Permission denied
FAIL
[1] FALSE

bedr documentation built on May 2, 2019, 11:36 a.m.