From f7bd3336deccdd623f396c9a083d9257624a42e5 Mon Sep 17 00:00:00 2001
From: Al-Murphy <alanmurph94@hotmail.com>
Date: Thu, 22 Feb 2024 09:03:48 +0000
Subject: [PATCH] longtests upstream

---
 DESCRIPTION                                 |  2 +-
 tests/testthat/test-check_imputation_cols.R | 79 ---------------------
 2 files changed, 1 insertion(+), 80 deletions(-)
 delete mode 100644 tests/testthat/test-check_imputation_cols.R

diff --git a/DESCRIPTION b/DESCRIPTION
index f673655..a531936 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.11.7
+Version: 1.11.8
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",
diff --git a/tests/testthat/test-check_imputation_cols.R b/tests/testthat/test-check_imputation_cols.R
deleted file mode 100644
index cc901bb..0000000
--- a/tests/testthat/test-check_imputation_cols.R
+++ /dev/null
@@ -1,79 +0,0 @@
-test_that("Check that imputation columns added correctly", {
-  ## The following test uses more than 2GB of memory, which is more
-  ## than what 32-bit Windows can handle:
-  is_32bit_windows <- .Platform$OS.type == "windows" #&&
-  #.Platform$r_arch == "i386"
-  if (!is_32bit_windows) {
-    pth <- system.file("extdata", "eduAttainOkbay.txt",
-                       package = "MungeSumstats"
-    )
-    #only run not on linux to speed up linux bioc checks
-    if (Sys.info()["sysname"]!="Linux"){
-      eduAttainOkbay <- data.table::fread(pth)
-      # edit to make an rs id be imputed
-      eduAttainOkbay[1, "MarkerName"] <-
-        substring(
-          eduAttainOkbay[1, "MarkerName"], 3,
-          nchar(eduAttainOkbay[1, "MarkerName"])
-        )
-      # write to temp dir
-      file <- tempfile()
-      data.table::fwrite(eduAttainOkbay, file)
-      # run
-      reformatted <- MungeSumstats::format_sumstats(file,
-                                                    ref_genome = "GRCh37",
-                                                    compute_z = TRUE,
-                                                    compute_n = 1001,
-                                                    save_format='LDSC',
-                                                    imputation_ind = TRUE,
-                                                    allele_flip_check = TRUE,
-                                                    dbSNP=144
-      )
-      res <- data.table::fread(reformatted)
-      col_headers <- names(res)
-      imputat_cols <- c(
-        col_headers[grepl("^IMPUTATION_", col_headers)],
-        "flipped"["flipped" %in% col_headers],
-        col_headers[grepl("^convert_", col_headers)]
-      )
-      # just check imputation columns exist
-      expect_equal(length(imputat_cols) > 0, TRUE)
-      # also check all have at least 1 value present
-      have_value <- TRUE
-      for (col_i in imputat_cols) {
-        col_i_val <- res[[col_i]]
-        if (length(col_i_val[!is.na(col_i_val)]) == 0) {
-          have_value <- FALSE
-        }
-      }
-      expect_equal(have_value, TRUE)
-    } else{
-      expect_equal(isTRUE(Sys.info()["sysname"]=="Linux"), TRUE)
-      expect_equal(isTRUE(Sys.info()["sysname"]=="Linux"), TRUE)
-    }
-    # check other compute_n values
-    eduAttainOkbay <- data.table::fread(pth)
-    eduAttainOkbay[, N_CON := 100]
-    eduAttainOkbay[, N_CAS := 120]
-    # write to temp dir
-    file <- tempfile()
-    data.table::fwrite(eduAttainOkbay, file)
-    methods <- c("ldsc", "sum", "giant", "metal")
-    reformatted <- MungeSumstats::format_sumstats(file,
-                                                  ref_genome = "GRCh37",
-                                                  compute_n = methods,
-                                                  on_ref_genome = FALSE,
-                                                  strand_ambig_filter = FALSE,
-                                                  bi_allelic_filter = FALSE,
-                                                  allele_flip_check = FALSE,
-                                                  dbSNP=144
-    )
-    res <- data.table::fread(reformatted)
-    expect_equal(all(paste0("Neff_", c("ldsc", "giant", "metal")) %in%
-                       colnames(res)), TRUE)
-  } else {
-    expect_equal(is_32bit_windows, TRUE)
-    expect_equal(is_32bit_windows, TRUE)
-    expect_equal(is_32bit_windows, TRUE)
-  }
-})