Fixed several linting issues

tests/testthat/test-admix1.R

@@ -46,7 +46,6 @@ test_that("type convertions behave like on Matlab", {
   expect_equal(proportion2str(0.4), "0.40")
   expect_equal(proportion2str(0.89), "0.89")
   expect_equal(proportion2str(-0.4), "0.0-40") # also bugged in original
-  # TODO: fix after release, as long as it doesn't break anything else
 })
 
 test_that("computeRows behaves like on Matlab", {

tests/testthat/test-greedyMix.R

@@ -1,11 +1,7 @@
 context("Auxiliary functions to greedyMix")
 
 # Defining the relative path to current inst -----------------------------------
-if (interactive()) {
-  path_inst <- "../../inst/ext"
-} else {
-  path_inst <- system.file("ext", "", package = "rBAPS")
-}
+path_inst <- system.file("ext", "", package = "rBAPS")
 
 # Reading datasets -------------------------------------------------------------
 baps_diploid <- read.delim(
@@ -50,7 +46,6 @@ df_bam <- greedyMix(
   data    = file.path(path_inst, "bam_example.bam"),
   format  = "BAM",
 )
-# TODO #19: add example reading Genpop
 test_that("Files are imported correctly", {
   expect_equal(dim(df_fasta), c(5, 99))
   expect_equal(dim(df_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))

tests/testthat/test-greedyPopMix.R

@@ -15,7 +15,7 @@ test_that("Auxiliary functions work properly", {
   expect_equal(
     getPopDistancesByKL(x2),
     list(
-      Z = matrix(c(c(1, 101:198), c(2:100), rep(0, 99)), nrow = 99, ncol = 3),
+      Z = matrix(c(c(1, 101:198), 2:100, rep(0, 99)), nrow = 99, ncol = 3),
       distances = as.matrix(rep(0, 4950))
     )
   )
@@ -27,7 +27,7 @@ test_that("Auxiliary functions work properly", {
     rows        = matrix(c(1: 3, 1: 3), 3),
     alleleCodes = matrix(c(1, 4, 9, 2, 5, 8), 3),
     noalle      = matrix(c(3, 3), 1),
-    adjprior    = matrix(rep(3/9, 6), 3),
+    adjprior    = matrix(rep(3 / 9, 6), 3),
     priorTerm   = 5.9125
   )
   expect_equal(handlePopData(x3), y3, tol = 1e-4)