Preparing gateR 0.1.1 for submission

gateR 0.1.0 did not pass the incoming CRAN checks automatically Flavor: r-devel-windows-ix86+x86_64 Check: Overall checktime, Result: NOTE Overall checktime 16 min > 10 min Flavor: r-devel-linux-x86_64-debian-gcc Check: CRAN incoming feasibility, Result: NOTE Maintainer: 'Ian D. Buller <[email protected]>' New submission Possibly mis-spelled words in DESCRIPTION: Bithell (38:63, 40:24) Cytometry (3:57) al (37:57) et (37:54) immunologically (32:19) ------ The mis-spelled words can be safely ignored. However, reduced the checktime by streamlining the examples and testthat Changed example in gating() by changing from \donttest{} to if (interactive()) {} Streamlined the number of "[it] works" tests in testthat for gating(), lotrrs(), and rrs() Updated cran-comments.md for CRAN resubmission Added CRAN-RELEASE to .Rbuildignore
lance-waller-lab · Oct 29, 2020 · daf194c · daf194c
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -4,3 +4,4 @@
 ^cran-comments\.md$
 ^vignette\.Rmd$
 ^dev$
+^CRAN-RELEASE$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gateR
 Type: Package
 Title: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation
-Version: 0.1.0
-Date: 2020-10-28
+Version: 0.1.1
+Date: 2020-10-29
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",

diff --git a/R/gating.R b/R/gating.R
@@ -55,15 +55,15 @@
 #' @export
 #' 
 #' @examples
-#' \donttest{
+#' if (interactive()) {
 #' # Use 'extdata' from the {flowWorkspaceData} package
 #'   flowDataPath <- system.file("extdata", package = "flowWorkspaceData")
 #'   fcsFiles <- list.files(pattern = "CytoTrol", flowDataPath, full = TRUE)
 #'   ncfs  <- ncdfFlow::read.ncdfFlowSet(fcsFiles)
 #'   fr1 <- ncfs[[1]]
 #'   fr2 <- ncfs[[2]]
 #' 
-#' ## Comparison of two samples (single condition) "g1"
+#' # Comparison of two samples (single condition) "g1"
 #' ## Two gates (four markers) "CD4", "CD38", "CD8", and "CD3"
 #' ## Log10 Transformation for both markers
 #' ## Remove cells with NA and Inf values

diff --git a/R/lotrrs.R b/R/lotrrs.R
@@ -52,7 +52,7 @@
 #'   fr1 <- ncfs[[1]]
 #'   fr2 <- ncfs[[2]]
 #' 
-#' ## Comparison of two samples at two time points (two conditions) "g1" and "g2"
+#' # Comparison of two samples at two time points (two conditions) "g1" and "g2"
 #' ## (Create a random binary variable for "g2")
 #' ## One gate (two markers) "CD4", "CD38"
 #' ## Log10 Transformation for both markers

diff --git a/R/rrs.R b/R/rrs.R
@@ -46,7 +46,7 @@
 #'   fr1 <- ncfs[[1]]
 #'   fr2 <- ncfs[[2]]
 #' 
-#' ## Comparison of two samples (single condition) "g1"
+#' # Comparison of two samples (single condition) "g1"
 #' ## One gate (two markers) "CD4", "CD38"
 #' ## Log10 Transformation for both markers
 #' ## Remove cells with NA and Inf values

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,4 +1,9 @@
-## This is a new release
+## This is the first resubmission
+
+* Actions taken regarding feedback from CRAN teams' auto-check service
+  * Reduced overall checktime by changing example in gating() by changing from \donttest{} to if (interactive()) {}
+  * Reduced overall checktime by streamlining the number of "[it] works" tests in testthat for gating(), lotrrs(), and rrs()
+  * Note about "Possibly mis-spelled words in DESCRIPTION" can be safely ignored
 
 ## Test environments
 * local OS X install, R 3.6.3
@@ -16,8 +21,15 @@ There was 1 NOTE:
   * Cytometry (3:57)
   * al (37:57)
   * et (37:54)
+  * immunologically (32:19)
 
 ## R CMD check results
 0 errors | 0 warnings | 0 notes
 
+* Duration
+  * local OS X install, R 3.6.3: 99 seconds
+  * win-builder, devel: 584 seconds (under 10 minutes)
+  * win-builder, oldrelease: 530 seconds
+  * win-builder, release: 620 seconds
+
 ## Submitted by Maintainer
diff --git a/dev/build.R b/dev/build.R
@@ -24,7 +24,7 @@ use_test()
 test()
 
 # NAMESPACE
-document()
+devtools::document()
 install()
 
 # Check

diff --git a/man/gating.Rd b/man/gating.Rd
diff --git a/tests/testthat/test-gating.R b/tests/testthat/test-gating.R
@@ -80,13 +80,13 @@ test_that("gating throws error with invalid arguments", {
            p_correct = "none")
   )
 
-  expect_error(
-    gating(dat = fubar,
-           vars = c("log10_CD4", "log10_CD38",
-                    "log10_CD8", "log10_CD3"),
-           n_condition = 2,
-           p_correct = "none")
-  )
+  # expect_error(
+  #   gating(dat = fubar,
+  #          vars = c("log10_CD4", "log10_CD38",
+  #                   "log10_CD8", "log10_CD3"),
+  #          n_condition = 2,
+  #          p_correct = "none")
+  # )
 
   # Non-binary third feature
   expect_error(
@@ -167,53 +167,53 @@ test_that("gating works", {
            p_correct = "none")
   )
 
-  expect_named(
-    gating(dat = obs_dat,
-           vars = c("log10_CD4", "log10_CD38",
-                    "log10_CD8", "log10_CD3"),
-           n_condition = 2,
-           p_correct = "none")
-  )
-
-#   expect_named(
-#     gating(dat = obs_dat,
-#            vars = c("log10_CD4", "log10_CD38"),
-#            n_condition = 1,
-#            alpha = 0.1,
-#            p_correct = "none")
-#   )
-# 
-#   expect_named(
-#     gating(dat = obs_dat,
-#            vars = c("log10_CD4", "log10_CD38"),
-#            n_condition = 1,
-#            alpha = 0.01,
-#            p_correct = "none")
-#   )
-# 
-#   expect_named(
-#     gating(dat = obs_dat,
-#            vars = c("log10_CD4", "log10_CD38"),
-#            n_condition = 1,
-#            numerator = FALSE,
-#            p_correct = "none")
-#   )
-# # 
-#   expect_named(
-#     gating(dat = obs_dat,
-#            vars = c("log10_CD4", "log10_CD38"),
-#            n_condition = 2,
-#            doplot = TRUE,
-#            rcols = c("green", "yellow", "purple"),
-#            p_correct = "none")
-#   )
-#   
-#   expect_named(
-#     gating(dat = obs_dat,
-#            vars = c("log10_CD4", "log10_CD38"),
-#            n_condition = 1,
-#            resolution = 40,
-#            p_correct = "correlated")
-#   )
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38",
+  #                   "log10_CD8", "log10_CD3"),
+  #          n_condition = 2,
+  #          p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38"),
+  #          n_condition = 1,
+  #          alpha = 0.1,
+  #          p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38"),
+  #          n_condition = 1,
+  #          alpha = 0.01,
+  #          p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38"),
+  #          n_condition = 1,
+  #          numerator = FALSE,
+  #          p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38"),
+  #          n_condition = 2,
+  #          doplot = TRUE,
+  #          rcols = c("green", "yellow", "purple"),
+  #          p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38"),
+  #          n_condition = 1,
+  #          resolution = 40,
+  #          p_correct = "correlated")
+  # )
 }
 )
diff --git a/tests/testthat/test-lotrrs.R b/tests/testthat/test-lotrrs.R
@@ -70,7 +70,6 @@ test_that("lotrrs throws error with invalid arguments", {
            p_correct = "none")
   )
 
-
   # Incorrectly specified alpha
   expect_error(
     lotrrs(dat = obs_dat,
@@ -89,22 +88,22 @@ test_that("lotrrs throws error with invalid arguments", {
 
 test_that("lotrrs works", {
 
-  expect_named(
-    lotrrs(dat = obs_dat,
-        p_correct = "none")
-  )
+  # expect_named(
+  #   lotrrs(dat = obs_dat,
+  #       p_correct = "none")
+  # )
 
   expect_named(
     lotrrs(dat = obs_dat,
         p_correct = "uncorrelated")
   )
 
-  expect_named(
-    lotrrs(dat = obs_dat,
-        resolution = 40,
-        p_correct = "correlated")
-  )
-
+  # expect_named(
+  #   lotrrs(dat = obs_dat,
+  #       resolution = 40,
+  #       p_correct = "correlated")
+  # )
+  # 
   # expect_named(
   #   lotrrs(dat = obs_dat,
   #       alpha = 0.1,

diff --git a/tests/testthat/test-rrs.R b/tests/testthat/test-rrs.R
@@ -80,22 +80,22 @@ test_that("rrs throws error with invalid arguments", {
 
 test_that("rrs works", {
 
-  expect_named(
-    rrs(dat = obs_dat,
-        p_correct = "none")
-  )
+  # expect_named(
+  #   rrs(dat = obs_dat,
+  #       p_correct = "none")
+  # )
 
   expect_named(
     rrs(dat = obs_dat,
         p_correct = "uncorrelated")
   )
 
-  expect_named(
-    rrs(dat = obs_dat,
-        resolution = 40,
-        p_correct = "correlated")
-  )
-
+  # expect_named(
+  #   rrs(dat = obs_dat,
+  #       resolution = 40,
+  #       p_correct = "correlated")
+  # )
+  #
   # expect_named(
   #   rrs(dat = obs_dat,
   #       alpha = 0.1,