Temporary fix for vroom issue tidyverse/vroom#519

Shians · Oct 17, 2023 · 9242ccb · 9242ccb
1 parent f366823
commit 9242ccb
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Showing 7 changed files with 7 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: NanoMethViz
 Type: Package
 Title: Visualise methlation data from Oxford Nanopore sequencing
-Version: 2.7.9
+Version: 2.7.10
 Authors@R: c(
     person("Shian", "Su", email = "[email protected]", role = c("cre", "aut")))
 Description: NanoMethViz is a toolkit for visualising methylation data from 

diff --git a/NAMESPACE b/NAMESPACE
@@ -126,6 +126,7 @@ importFrom(readr,col_double)
 importFrom(readr,col_integer)
 importFrom(readr,col_logical)
 importFrom(readr,cols)
+importFrom(readr,local_edition)
 importFrom(readr,read_tsv)
 importFrom(rlang,.data)
 importFrom(scales,cut_si)

diff --git a/R/NanoMethViz-package.R b/R/NanoMethViz-package.R
@@ -8,7 +8,7 @@
 #' @importFrom dplyr %>%
 #' @importFrom methods new .valueClassTest is
 #' @importFrom rlang .data
-#' @importFrom readr read_tsv
+#' @importFrom readr read_tsv local_edition
 #' @importFrom ggplot2 aes geom_rect geom_segment geom_text ggplot theme_void
 #'   xlim ylim ggplot_build rel unit geom_vline
 #' @importFrom dplyr filter group_by ungroup inner_join mutate n select summarise case_when

diff --git a/R/convert_methy_format.R b/R/convert_methy_format.R
@@ -170,7 +170,7 @@ convert_methy_format <- function(
                 scipen = 999L
             )
         }
-
+        readr::local_edition(1) # temporary fix for vroom bad value
         readr::read_tsv_chunked(
             element$file,
             col_types = col_types,

diff --git a/R/filter_methy.R b/R/filter_methy.R
@@ -61,7 +61,7 @@ filter_methy <- function(x, output_file, ...) {
             scipen = 999L
         )
     }
-
+    readr::local_edition(1) # temporary fix for vroom bad value
     readr::read_tsv_chunked(
         input_file,
         callback = readr::SideEffectChunkCallback$new(writer_fn),

diff --git a/R/methy_to_bsseq.R b/R/methy_to_bsseq.R
@@ -73,6 +73,7 @@ convert_methy_to_dss <- function(
 #' @importFrom dplyr select distinct arrange mutate
 #' @importFrom bsseq BSseq
 create_bsseq_from_files <- function(paths, samples, verbose = TRUE) {
+    readr::local_edition(1) # temporary fix for vroom bad value
     read_dss <- purrr::partial(
         read_tsv,
         col_types = cols(

diff --git a/R/query_methy.R b/R/query_methy.R
@@ -210,6 +210,7 @@ query_methy_tabix <- function(x, chr, start, end, force) {
         }
 
         # using readr::read_tsv on character vectors seems to leak memory
+        # readr::local_edition(1) # temporary fix for vroom bad value
         as_tibble(
             utils::read.table(
                 textConnection(x),