Preparation for CRAN release

Reduced the number of redunant tests in testthat (commented out, not deleted) Updated language in vignette.Rmd to clarify conditions, variables, and features Removed vignette_cache and set cache = FALSE to reduce size of package Initial commit of cran-comments.md (and .Rbuildignore entry) Initial commit of NEWS.md Moved /figures into /man so README.md can read them during build Moved gator.png to /dev Updated date and version number (0.1.0)
lance-waller-lab · Oct 28, 2020 · 3dd10f8 · 3dd10f8
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,5 +1,6 @@
 ^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^cran-comments\.md$
 ^vignette\.Rmd$
 ^dev$
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: 0.1.0.9000
-Date: 2020-10-27
+Version: 0.1.0
+Date: 2020-10-28
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",

diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1 @@
+# gateR (development version)
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-gateR: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation <img src="dev/figures/gateR.png" width="120" align="right" />
+gateR: Statistical Gating Application for Flow and Mass Cytometry Analysis via Spatial Kernel Density Estimation <img src="man/figures/gateR.png" width="120" align="right" />
 ===================================================
 
 <h2 id="overview">
@@ -176,11 +176,11 @@ graphics::legend("topright",
                  bty = "n")
 ```
 
-![](dev/figures/gate1.png)
+![](man/figures/gate1.png)
 
-![](dev/figures/gate2.png)
+![](man/figures/gate2.png)
 
-![](dev/figures/postgate.png)
+![](man/figures/postgate.png)
 
 ```r
 # ----------------------------- #

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,23 @@
+## This is a new release
+
+## Test environments
+* local OS X install, R 3.6.3
+* win-builder, (devel, oldrelease, release)
+* Rhub
+  * Fedora Linux, R-devel, clang, gfortran
+  * Ubuntu Linux 16.04 LTS, R-release, GCC
+  * Windows Server 2008 R2 SP1, R-devel, 32⁄64 bit
+  * Debian Linux, R-devel, GCC
+
+There was 1 NOTE:
+
+* Possibly mis-spelled words in DESCRIPTION:
+  * Bithell (38:63, 40:24)
+  * Cytometry (3:57)
+  * al (37:57)
+  * et (37:54)
+
+## R CMD check results
+0 errors | 0 warnings | 0 notes
+
+## Submitted by Maintainer
diff --git a/dev/build.R b/dev/build.R
@@ -35,11 +35,16 @@ usethis::use_build_ignore(c("build"))
 usethis::use_build_ignore(c("figures"))
 
 # rhub
-rhub::validate_email()
+devtools::check_rhub()
 rhub::check_for_cran()
 
 # Check on windows
 devtools::check_win_devel()
+devtools::check_win_oldrelease()
+devtools::check_win_release()
+
+# Release to CRAN
+#devtools::release()
 
 # Example in README
 # ------------------ #

diff --git a/dev/figures/gator.png → dev/gator.png b/dev/figures/gator.png → dev/gator.png
diff --git a/dev/hexsticker_gateR.R b/dev/hexsticker_gateR.R
@@ -16,7 +16,7 @@
 library(hexSticker)
 
 # Image file
-path_image <- "./man/figures/gator.png"
+path_image <- "./dev/gator.png"
 
 # Create hexSticker
 ## the alligator palette https://www.color-hex.com/color-palette/33955

diff --git a/dev/figures/gate1.png → man/figures/gate1.png b/dev/figures/gate1.png → man/figures/gate1.png
diff --git a/dev/figures/gate2.png → man/figures/gate2.png b/dev/figures/gate2.png → man/figures/gate2.png
diff --git a/dev/figures/gateR.png → man/figures/gateR.png b/dev/figures/gateR.png → man/figures/gateR.png
diff --git a/dev/figures/postgate.png → man/figures/postgate.png b/dev/figures/postgate.png → man/figures/postgate.png
diff --git a/tests/testthat/test-gating.R b/tests/testthat/test-gating.R
@@ -138,26 +138,26 @@ test_that("gating throws error with invalid arguments", {
 
 test_that("gating works", {
 
-  expect_named(
-      gating(dat = obs_dat,
-             vars = c("log10_CD4", "log10_CD38"),
-             n_condition = 1,
-             p_correct = "none")
-  )
-
-  expect_named(
-    gating(dat = obs_dat,
-           vars = c("log10_CD4", "log10_CD38"),
-           n_condition = 2,
-           p_correct = "none")
-  )
-
-  expect_named(
-    gating(dat = obs_dat,
-           vars = c("log10_CD4", "log10_CD38"),
-           n_condition = 1,
-           p_correct = "uncorrelated")
-  )
+  # expect_named(
+  #     gating(dat = obs_dat,
+  #            vars = c("log10_CD4", "log10_CD38"),
+  #            n_condition = 1,
+  #            p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38"),
+  #          n_condition = 2,
+  #          p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   gating(dat = obs_dat,
+  #          vars = c("log10_CD4", "log10_CD38"),
+  #          n_condition = 1,
+  #          p_correct = "uncorrelated")
+  # )
 
   expect_named(
     gating(dat = obs_dat,
@@ -175,45 +175,45 @@ test_that("gating works", {
            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"),
+#            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
@@ -105,17 +105,30 @@ test_that("lotrrs works", {
         p_correct = "correlated")
   )
 
-  expect_named(
-    lotrrs(dat = obs_dat,
-        alpha = 0.01,
-        p_correct = "none")
-  )
-
-  expect_named(
-    lotrrs(dat = obs_dat,
-        doplot = TRUE,
-        rcols = c("green", "yellow", "purple"),
-        p_correct = "none")
-  )
+  # expect_named(
+  #   lotrrs(dat = obs_dat,
+  #       alpha = 0.1,
+  #       p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   lotrrs(dat = obs_dat,
+  #       alpha = 0.01,
+  #       p_correct = "none")
+  # )
+  # 
+  # 
+  # expect_named(
+  #   lotrrs(dat = obs_dat,
+  #       doplot = TRUE,
+  #       p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   lotrrs(dat = obs_dat,
+  #       doplot = TRUE,
+  #       rcols = c("green", "yellow", "purple"),
+  #       p_correct = "none")
+  # )
 }
 )
diff --git a/tests/testthat/test-rrs.R b/tests/testthat/test-rrs.R
@@ -96,29 +96,29 @@ test_that("rrs works", {
         p_correct = "correlated")
   )
 
-  expect_named(
-    rrs(dat = obs_dat,
-        alpha = 0.1,
-        p_correct = "none")
-  )
-
-  expect_named(
-    rrs(dat = obs_dat,
-        alpha = 0.01,
-        p_correct = "none")
-  )
-
-  expect_named(
-    rrs(dat = obs_dat,
-        doplot = TRUE,
-        p_correct = "none")
-  )
-
-  expect_named(
-    rrs(dat = obs_dat,
-        doplot = TRUE,
-        rcols = c("green", "yellow", "purple"),
-        p_correct = "none")
-  )
+  # expect_named(
+  #   rrs(dat = obs_dat,
+  #       alpha = 0.1,
+  #       p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   rrs(dat = obs_dat,
+  #       alpha = 0.01,
+  #       p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   rrs(dat = obs_dat,
+  #       doplot = TRUE,
+  #       p_correct = "none")
+  # )
+  # 
+  # expect_named(
+  #   rrs(dat = obs_dat,
+  #       doplot = TRUE,
+  #       rcols = c("green", "yellow", "purple"),
+  #       p_correct = "none")
+  # )
 }
 )