Set data.table threads to 2 for package checks (#139)

* Seems to pass CRAN checks now (tested with rhub) * Submit v1.0.2
wincowgerDEV · Sep 5, 2023 · f4c2107 · f4c2107
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.1
-Date: 2023-09-04 13:32:12 UTC
-SHA: 0ae4952382c771ea3f729f1303fd6431182d7d95
+Version: 1.0.2
+Date: 2023-09-05 13:16:55 UTC
+SHA: 92ce663a7883e3c9886fb7c2ada24fd7deb4c49b
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: OpenSpecy
 Type: Package
 Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
-Version: 1.0.1
-Date: 2023-09-04
+Version: 1.0.2
+Date: 2023-09-05
 Authors@R: c(person("Win", "Cowger", role = c("cre", "aut", "dtc"),
       email = "wincowger@gmail.com",
       comment = c(ORCID = "0000-0001-9226-3104")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# OpenSpecy 1.0.2
+
+## Bug Fixes
+
+- Set data.table threads to 2 for (CRAN) checks
+
+
 # OpenSpecy 1.0.1
 
 ## Bug Fixes

diff --git a/R/def_features.R b/R/def_features.R
@@ -19,6 +19,7 @@
 #' collapsed for the features.
 #'
 #' @examples
+#' \dontshow{data.table::setDTthreads(2)}
 #' tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any()
 #' identified_map <- def_features(tiny_map, tiny_map$metadata$x == 0)
 #' collapse_spec(identified_map)

diff --git a/R/interactive_plots.R b/R/interactive_plots.R
@@ -41,6 +41,7 @@
 #' spectra from the \code{OpenSpecy} object(s).
 #'
 #' @examples
+#' \dontshow{data.table::setDTthreads(2)}
 #' data("raman_hdpe")
 #' tiny_map <- read_extdata("CA_tiny_map.zip") |> read_zip()
 #' plotly_spec(raman_hdpe)

diff --git a/R/read_multi.R b/R/read_multi.R
@@ -19,6 +19,7 @@
 #' All \code{read_*()} functions return \code{OpenSpecy} objects
 #'
 #' @examples
+#' \dontshow{data.table::setDTthreads(2)}
 #' read_extdata("raman_hdpe.csv") |> read_any()
 #' read_extdata("ftir_ldpe_soil.asp") |> read_any()
 #' read_extdata("testdata_zipped.zip") |> read_zip()

diff --git a/README.md b/README.md
@@ -102,5 +102,5 @@ Needs an Open Source Community: Open Specy to the Rescue!”
 [10.1021/acs.analchem.1c00123](https://doi.org/10.1021/acs.analchem.1c00123).
 
 Cowger W, Steinmetz Z (2023). “OpenSpecy: Analyze, Process,
-Identify, and Share Raman and (FT)IR Spectra.” *R package*, **1.0.1**.
+Identify, and Share Raman and (FT)IR Spectra.” *R package*, **1.0.2**.
 [https://github.com/wincowgerDEV/OpenSpecy-package](https://github.com/wincowgerDEV/OpenSpecy-package).
diff --git a/man/def_features.Rd b/man/def_features.Rd
diff --git a/man/interactive_plots.Rd b/man/interactive_plots.Rd
diff --git a/man/read_multi.Rd b/man/read_multi.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,4 +1,7 @@
 library(testthat)
 library(OpenSpecy)
 
+library(data.table)
+setDTthreads(2)
+
 test_check("OpenSpecy")
diff --git a/tests/testthat/test-adj_range.R b/tests/testthat/test-adj_range.R
@@ -1,5 +1,3 @@
-library(data.table)
-
 test_that("flatten_range() error handling", {
   test <- as_OpenSpecy(x = 1:10, spectra = data.table(V1 = 1:10))
 

diff --git a/tests/testthat/test-as_OpenSpecy.R b/tests/testthat/test-as_OpenSpecy.R
@@ -1,5 +1,3 @@
-library(data.table)
-
 data("raman_hdpe")
 df <- read_extdata("raman_hdpe.csv") |> read.csv()
 

diff --git a/tests/testthat/test-conform_spec.R b/tests/testthat/test-conform_spec.R
@@ -1,5 +1,3 @@
-library(data.table)
-
 data("raman_hdpe")
 
 test_that("conform_spec() throws an error for non-OpenSpecy objects", {

diff --git a/tests/testthat/test-gen_OpenSpecy.R b/tests/testthat/test-gen_OpenSpecy.R
@@ -1,4 +1,3 @@
-library(data.table)
 data("raman_hdpe")
 csv <- read_extdata("raman_hdpe.csv") |> read.csv()
 

diff --git a/tests/testthat/test-io_spec.R b/tests/testthat/test-io_spec.R
@@ -1,11 +1,9 @@
-# Loading test data
-data(raman_hdpe)
-
 # Create temp dir for testthat
 tmp <- file.path(tempdir(), "OpenSpecy-testthat")
 dir.create(tmp, showWarnings = F)
 
-library(data.table)
+# Loading test data
+data(raman_hdpe)
 
 test_that("extdata files are present", {
   ed <- read_extdata()

diff --git a/tests/testthat/test-manage_spec.R b/tests/testthat/test-manage_spec.R
@@ -1,4 +1,3 @@
-library(data.table)
 data("raman_hdpe")
 
 specs <- lapply(c(read_extdata("raman_hdpe.yml"),

diff --git a/tests/testthat/test-read_ext.R b/tests/testthat/test-read_ext.R
@@ -2,8 +2,6 @@
 tmp <- file.path(tempdir(), "OpenSpecy-testthat")
 dir.create(tmp, showWarnings = F)
 
-library(data.table)
-
 data("raman_hdpe")
 
 test_that("extdata files are present", {

diff --git a/vignettes/sop.Rmd b/vignettes/sop.Rmd
@@ -16,6 +16,8 @@ knitr::opts_chunk$set(
   comment = "#>",
   warning = FALSE
 )
+
+data.table::setDTthreads(2)
 ```
 
 # Document Overview 

diff --git a/vignettes/sop.html b/vignettes/sop.html