EOD

richelbilderbeek · Oct 18, 2022 · 8ecbffb · 8ecbffb
1 parent 88cded3
commit 8ecbffb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,7 +13,7 @@ Description:
     These answers are not published yet.
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Imports:
     data.table,
     dplyr,

diff --git a/R/calculate-overlap.R b/R/calculate-overlap.R
@@ -15,6 +15,9 @@ calculate_overlap <- function(
   protein_lengths_filename,
   tmh_overlapping_binders_as_data_filename
 ) {
+  tmh.9mers <- NULL; rm(tmh.9mers) # nolint, fixes warning: no visible binding for global variable
+
+
   load(tmh_9mers_as_data_filename) # Used to be load("work/tmh.9mers.Rdata")
   pldf <- utils::read.table(protein_lengths_filename, row.names=1 )
   pl <- pldf[,1]

diff --git a/R/correlate-to-hydrophobicity.R b/R/correlate-to-hydrophobicity.R
@@ -14,6 +14,8 @@ correlate_to_hydrophobicity <- function(
   tmh_overlapping_binders_as_data_filename,
   figure_1_d_filename
 ) {
+  r <- NULL; rm(r) # nolint, fixes warning: no visible binding for global variable
+
   testthat::expect_true(file.exists(tmh_overlapping_binders_as_data_filename))
 
   # loads 'r'

diff --git a/R/hydrophobe-controls.R b/R/hydrophobe-controls.R
@@ -13,6 +13,8 @@ hydrophobe_controls <- function(
   proteome_9mer_hydrophobicity_as_data_filename,
   tmh_9mers_as_data_filename
 ) {
+  tmh.9mers <- NULL; rm(tmh.9mers) # nolint, fixes warning: no visible binding for global variable
+
   load(proteome_9mer_hydrophobicity_as_data_filename) # Used to be 'load("work/proteome.9mer.hydrophobicity.Rdata")'
   load(tmh_9mers_as_data_filename) # Used to be load("work/tmh.9mers.Rdata")
 

diff --git a/R/hydrophobicity-distribution.R b/R/hydrophobicity-distribution.R
@@ -18,6 +18,8 @@ hydrophobicity_distribution <- function(
   kyte_doolittle_scale_as_data_filename,
   proteome_9mer_hydrophobicity_as_data_filename
 ) {
+  proteome <- NULL; rm(proteome) # nolint, fixes warning: no visible binding for global variable
+
   load(proteome_as_data_filename) # Used to be 'load("work/proteome.Rdata")'
   load(kyte_doolittle_scale_as_data_filename) # Used to be 'load("data/kyte.doolittle.scale.Rdata")'
 

diff --git a/R/simplify_haplotype_names.R b/R/simplify_haplotype_names.R
@@ -1,5 +1,6 @@
 #' Simplify haplotype names to numbers
 #' Will be NA for unknown haplotypes
+#' @inheritParams default_params_doc
 #' @export
 simplify_haplotype_names <- function(haplotype_names) {
   simple_haplotype_names <- rep(NA, length = length(haplotype_names))