ci: resolve conflict

gdrplatform · Mar 14, 2024 · c485ed8 · c485ed8
2 parents 708121c + 5bb13b9
commit c485ed8
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Showing 9 changed files with 23 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,8 +2,8 @@ Type: Package
 Package: gDRcore
 Title: Processing functions and interface to process and analyze drug
     dose-response data
-Version: 1.1.14
-Date: 2024-03-07
+Version: 1.1.15
+Date: 2024-03-14
 Authors@R: c(
     person("Bartosz", "Czech", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0002-9908-3007")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,9 @@
-## gDRcore 1.1.14 - 2024-03-07
+## gDRcore 1.1.15 - 2024-03-14
 * cleanup package
 
+## gDRcore 1.1.14 - 2024-03-12
+* update function description
+
 ## gDRcore 1.1.13 - 2024-02-26
 * improve pkgdown site
   * improved references

diff --git a/R/fit_SE.combinations.R b/R/fit_SE.combinations.R
@@ -27,7 +27,7 @@
 #' fit_SE.combinations(se1[1, 1])
 #'
 #' @keywords runDrugResponseProcessingPipeline
-#' @return A code{SummarizedExperiment} object with an additional assay 
+#' @return A \code{SummarizedExperiment} object with an additional assay 
 #' containing the combination metrics.
 #' 
 #' @export

diff --git a/R/utils.R b/R/utils.R
@@ -421,7 +421,7 @@ rbindParallelList <- function(x, name) {
 #' @param nomatch the value to be returned in the case when no match is found.
 #'   If not provided and \code{indexes=TRUE}, items with no match will be
 #'   represented as \code{NA}.  If set to \code{NULL}, items with no match will
-#'   be set to an index value of \code{length+1}.  If {indexes=FALSE}, they will
+#'   be set to an index value of \code{length+1}.  If \code{indexes=FALSE}, they will
 #'   default to \code{NA}.
 #' @details Source of the function: 
 #' https://github.com/cran/grr/blob/master/R/grr.R

diff --git a/man/fit_SE.combinations.Rd b/man/fit_SE.combinations.Rd
diff --git a/man/gDRcore-package.Rd b/man/gDRcore-package.Rd
diff --git a/man/grr_matches.Rd b/man/grr_matches.Rd
diff --git a/tests/testthat/test-runDrugResponseProcessingPipeline.R b/tests/testthat/test-runDrugResponseProcessingPipeline.R
@@ -39,7 +39,9 @@ test_that("main pipeline functions works as expected", {
     data_dir = p_dir
   )
   expect_true(length(list.files(p_dir)) > 0)
-  expect_length(mae_v1$warnings, 2)
+  expect_lte(length(mae_v1$warnings), 3)
+  expect_true(any(grepl("Switching into 'Barcode' nested confounder.", mae_v1$warnings)))
+  expect_true(any(grepl("method L-BFGS-B uses 'factr'.", mae_v1$warnings)))
 
   mae_v2 <-
     purrr::quietly(runDrugResponseProcessingPipeline)(
@@ -58,13 +60,17 @@ test_that("main pipeline functions works as expected", {
       start_from = "normalize_SE",
       selected_experiments = c("single-agent")
     )
-  expect_length(mae_v3$warnings, 2)
-
+  expect_lte(length(mae_v3$warnings), 3)
+  expect_true(any(grepl("Switching into 'Barcode' nested confounder.", mae_v3$warnings)))
+  expect_true(any(grepl("method L-BFGS-B uses 'factr'.", mae_v3$warnings)))
+
   mae_v4 <-
     purrr::quietly(runDrugResponseProcessingPipeline)(
       mae_v1$result
     )
   expect_lte(length(mae_v4$warnings), 3)
+  expect_true(any(grepl("Switching into 'Barcode' nested confounder.", mae_v3$warnings)))
+  expect_true(any(grepl("method L-BFGS-B uses 'factr'.", mae_v3$warnings)))
 
   expect_identical(mae_v1$result, mae_v2$result)
   expect_identical(mae_v2$result, mae_v3$result)

diff --git a/vignettes/gDRcore.Rmd b/vignettes/gDRcore.Rmd
@@ -16,7 +16,6 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup, echo = FALSE}
-library(gDRimport)
 library(gDRtestData)
 library(gDRcore)
 log_level <- futile.logger::flog.threshold("ERROR")