Merge 45c9f7f into b69fec8

.gitignore

@@ -13,3 +13,5 @@ pepr.Rproj
 docs
 doc
 Meta
+pepr.Rcheck/
+pepr_*.tar.gz

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.3.0
+Version: 0.3.1
 Date: 2020-05-26
 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org",
     role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre")))

NEWS.md

@@ -1,3 +1,7 @@
+# pepr 0.3.1 - 2020-05-26
+
+## Fixed
+
 # pepr 0.3.0 - 2020-05-26
 
 **This version introduced backwards-incompatible changes.**

R/config.R

@@ -186,7 +186,7 @@ setMethod(
   signature = "Config", 
   definition = function(object) {
     if (CFG_VERSION_KEY %in% names(object)){
-      split = str_split(object[[CFG_VERSION_KEY]],"\\.")[[1]]
+      split = strsplit(object[[CFG_VERSION_KEY]],"[.]")[[1]]
       if (length(split) < 3) stop("PEP version string is not tripartite")
       majorVer = as.numeric(split[1])
       if (majorVer < 2){
@@ -352,5 +352,5 @@ setMethod(
 #' @return string project name
 .inferProjectName = function(cfg, filename){
   if (!is.null(cfg$name)) return(cfg$name)
-  return(basename(dirname(normalizePath(filename))))
+  return(basename(dirname(path.expand(filename))))
 }

R/project.R

@@ -23,7 +23,7 @@ setMethod("initialize", "Project", function(.Object, ...) {
     ellipsis <- list(...)
     if (!is.null(ellipsis$file)) {
         # check if file path provided
-        .Object@file = .makeAbsPath(ellipsis$file, parent = getwd())
+        .Object@file = .makeAbsPath(ellipsis$file, parent = path.expand(getwd()))
         # instantiate config object and stick it in the config slot
         .Object@config = Config(ellipsis$file, ellipsis$amendments)
         .Object = .loadSampleAnnotation(.Object)

R/utils.R

@@ -47,9 +47,9 @@
       if (!startsWith(path, "/") && length(undefinedID) == 0) {
         path = paste0("/", path)
       }
-      # prevent double slashes
-      path = gsub("//", "/", path)
     }
+    # prevent double slashes
+    path = gsub("//", "/", path)
   }
 
   # handle null/empty input.
@@ -58,7 +58,7 @@
   }
 
   # if it's a path, make it absolute
-  path = normalizePath(path.expand(path),mustWork = FALSE)
+  path = path.expand(path)
   # search for env vars, both bracketed and not 
   matchesBracket = gregexpr("\\$\\{\\w+\\}", path, perl=T)
   matches = gregexpr("\\$\\w+", path, perl=T)
@@ -131,7 +131,7 @@
   if (.isAbsolute(perhapsRelative)) {
     abspath = perhapsRelative
   } else {
-    abspath = file.path(normalizePath(parent), perhapsRelative)
+    abspath = file.path(path.expand(parent), perhapsRelative)
   }
   if (!.isAbsolute(abspath)) 
     stop("Relative path ", perhapsRelative, " and parent ", parent ,
@@ -151,8 +151,7 @@
 #' @return Flag indicating whether the \code{path} appears to be absolute.
 .isAbsolute = function(path) {
   if (!is.character(path)) stop("The path must be character")
-  firstChar = substr(path, 1, 1)
-  return(identical("/", firstChar) | identical("~", firstChar))
+  return(grepl("^(/|[A-Za-z]:|\\\\|~)", path))
 }
 
 .safeFileExists = function(path) {

tests/testthat/test_config.R

@@ -53,8 +53,7 @@ configConst = system.file(
 
 .isAbsolute = function(path) {
     if (!is.character(path)) stop("The path must be character")
-    firstChar = substr(path, 1, 1)
-    return(identical("/", firstChar) | identical("~", firstChar))
+    return(grepl("^(/|[A-Za-z]:|\\\\|~)", path))
 }
 
 # tests -------------------------------------------------------------------
@@ -83,7 +82,7 @@ test_that("loadConfig returns correct object type", {
 
 test_that("loadConfig throws errors", {
     expect_error(Config("a"))
-    expect_error(Config(filename = Project(cfg)@config$sample_table))
+    expect_error(Config(Project(cfg)@config$sample_table))
 })
 
 test_that("paths are automatically expanded", {