get rid of vroom for the moment

waldronlab · Oct 28, 2023 · fed15c2 · fed15c2
1 parent ec37664
commit fed15c2
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Showing 5 changed files with 16 additions and 12 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: bugsigdbr
-Version: 1.8.0
+Version: 1.8.1
 Title: R-side access to published microbial signatures from BugSigDB
 Authors@R: c(
     person(given = "Ludwig",
@@ -26,7 +26,6 @@ Depends: R (>= 4.1)
 Imports:
     BiocFileCache,
     methods,
-    vroom,
     utils
 Suggests:
     BiocStyle,

diff --git a/NAMESPACE b/NAMESPACE
@@ -12,4 +12,5 @@ export(subsetByOntology)
 export(writeGMT)
 importFrom(methods,is)
 importFrom(utils,browseURL)
+importFrom(utils,read.csv)
 importFrom(utils,relist)
diff --git a/R/bugsigdb.R b/R/bugsigdb.R
@@ -48,6 +48,7 @@
 #'
 #'  df <- importBugSigDB()
 #'
+#' @importFrom utils read.csv
 #' @export
 importBugSigDB <- function(version = "10.5281/zenodo.6468009", cache = TRUE)
 {
@@ -82,11 +83,12 @@ importBugSigDB <- function(version = "10.5281/zenodo.6468009", cache = TRUE)
 
 .getdf <- function(from, to)
 {
-    dat <- suppressWarnings(vroom::vroom(from, skip = 1L,
-                                         altrep = FALSE, 
-                                         progress = FALSE,
-                                         show_col_types = FALSE))
-    dat <- as.data.frame(dat)
+#    dat <- suppressWarnings(vroom::vroom(from, skip = 1L,
+#                                         altrep = FALSE, 
+#                                         progress = FALSE,
+#                                         show_col_types = FALSE))
+#    dat <- as.data.frame(dat)
+    dat <- read.csv(from, skip = 1, check.names = FALSE)
     dat[["MetaPhlAn taxon names"]] <- strsplit(dat[["MetaPhlAn taxon names"]], ",")
     dat[["NCBI Taxonomy IDs"]] <- strsplit(dat[["NCBI Taxonomy IDs"]], ";")
 

diff --git a/R/getSignatures.R b/R/getSignatures.R
@@ -491,8 +491,9 @@ writeGMT <- function(sigs, gmt.file, ...) {
                       mic_int = "microbiome_int",
                       env = "environment")
     ma.url <- paste0(ma.url, lib, ".csv")
-    cont <- vroom::vroom(ma.url)
-    cont <- as.data.frame(cont)
+    #cont <- vroom::vroom(ma.url)
+    #cont <- as.data.frame(cont)
+    cont <- read.csv(ma.url, check.names = FALSE)
     rel.cols <- c("name", "member", "abund_change")
     cont <- cont[, rel.cols]
 

diff --git a/tests/testthat/test-importBugSigDB.R b/tests/testthat/test-importBugSigDB.R
@@ -5,9 +5,10 @@ checkImport <- function(bsdb, url)
     expect_gt(ncol(bsdb), 40)
     expect_true(all(c("Study", "Study design", "PMID") %in% colnames(bsdb)[1:4]))
 
-    dat <- suppressWarnings(vroom::vroom(url, skip = 1L, progress = FALSE,
-                                         show_col_types = FALSE))
-    dat <- as.data.frame(dat)
+    #dat <- suppressWarnings(vroom::vroom(url, skip = 1L, progress = FALSE,
+    #                                     show_col_types = FALSE))
+    #dat <- as.data.frame(dat)
+    dat <- read.csv(url, skip = 1, check.names = FALSE)
     dat[["MetaPhlAn taxon names"]] <- strsplit(dat[["MetaPhlAn taxon names"]],
                                                ",")
     dat[["NCBI Taxonomy IDs"]] <- strsplit(dat[["NCBI Taxonomy IDs"]], ";")