Browse code

Update to v 1.3.4

Giulia Pais authored on 03/08/2021 16:44:36
Showing11 changed files

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@@ -1,6 +1,6 @@
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 Package: ISAnalytics
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 Title: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
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-Version: 1.3.3
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+Version: 1.3.4
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 Date: 2020-07-03
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 Authors@R: c(
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   person(given = "Andrea",
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@@ -1,6 +1,13 @@
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 NEWS
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 ================
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+# ISAnalytics 1.3.4 (2021-08 -03)
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+
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+## FIXES/MINOR UPDATES
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+
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+-   Fixed issue in tests that lead to broken build
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+-   Slightly modified included data set for better examples
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+
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 # ISAnalytics 1.3.3 (2021-07-30)
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 ## MAJOR CHANGES
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 #' Example of imported multi-quantification integration matrices.
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 #'
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-#' The data was obtain by random sampling and anonimization of real research
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+#' The data was obtained manually by simulating real research
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 #' data.
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 #'
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 #' @usage data("integration_matrices")
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 #'
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-#' @format Data frame with 1547 rows and 8 columns
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+#' @format Data frame with 1689 rows and 8 columns
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 #' \describe{
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 #'  \item{chr}{The chromosome number (as character)}
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 #'  \item{integration_locus}{Number of the base at
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 #' Example of association file.
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 #'
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-#' The data was obtain by random sampling and anonimization of real research
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+#' The data was obtained manually by simulating real research
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 #' data.
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 #'
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 #' @usage data("association_file")
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@@ -1113,6 +1113,7 @@ sharing_heatmap <- function(sharing_df,
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 #' @export
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 #'
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 #' @examples
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+#' \donttest{
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 #' data("integration_matrices", package = "ISAnalytics")
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 #' data("association_file", package = "ISAnalytics")
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 #' aggreg <- aggregate_values_by_key(
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@@ -1127,6 +1128,7 @@ sharing_heatmap <- function(sharing_df,
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 #'     track_colors = c("navyblue", "gold"),
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 #'     grDevice = "default", track.height = 0.1
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 #' )
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+#' }
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 circos_genomic_density <- function(data,
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     gene_labels = NULL,
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     label_col = NULL,
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@@ -137,6 +137,13 @@ options("ISAnalytics.reports" = TRUE)
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 Show more
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 </summary>
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+# ISAnalytics 1.3.4 (2021-08 -03)
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+
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+## FIXES/MINOR UPDATES
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+
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+-   Fixed issue in tests that lead to broken build
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+-   Slightly modified included data set for better examples
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+
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 # ISAnalytics 1.3.3 (2021-07-30)
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 ## MAJOR CHANGES
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Binary files a/data/integration_matrices.RData and b/data/integration_matrices.RData differ
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Binary files a/inst/extdata/fs.zip and b/inst/extdata/fs.zip differ
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@@ -17,7 +17,7 @@ To generate an empty association file to fill see the
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 \code{generate_blank_association_file()} function.
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 }
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 \details{
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-The data was obtain by random sampling and anonimization of real research
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+The data was obtained manually by simulating real research
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 data.
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 }
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 \seealso{
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@@ -69,6 +69,7 @@ otherwise an error message is thrown.
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 }
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 }
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 \examples{
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+\donttest{
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 data("integration_matrices", package = "ISAnalytics")
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 data("association_file", package = "ISAnalytics")
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 aggreg <- aggregate_values_by_key(
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@@ -84,3 +85,4 @@ circos_genomic_density(by_subj,
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     grDevice = "default", track.height = 0.1
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 )
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 }
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+}
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 \alias{integration_matrices}
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 \title{Example of imported multi-quantification integration matrices.}
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 \format{
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-Data frame with 1547 rows and 8 columns
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+Data frame with 1689 rows and 8 columns
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 \describe{
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 \item{chr}{The chromosome number (as character)}
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 \item{integration_locus}{Number of the base at
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@@ -22,7 +22,7 @@ which the viral insertion occurred}
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 data("integration_matrices")
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 }
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 \description{
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-The data was obtain by random sampling and anonimization of real research
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+The data was obtained manually by simulating real research
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 data.
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 }
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 \keyword{datasets}
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@@ -155,7 +155,8 @@ test_that(paste(func_name, "reads type NEW different params"), {
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     expect_true(typeof(df$Value) %in% c("double", "integer"))
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     expect_true(all(df$CompleteAmplificationID %in% c("id3", "id4")))
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-    readr::write_tsv(sample_df %>% dplyr::select(-GeneName, -GeneStrand), tf)
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+    tf2 <- withr::local_tempfile(fileext = ".tsv")
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+    readr::write_tsv(sample_df %>% dplyr::select(-GeneName, -GeneStrand), tf2)
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     expected_summary_msg <- .summary_ism_import_msg(
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         "NEW",
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         FALSE,
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                     withr::with_file(
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                         file = tf,
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                         code = {
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-                            df <- import_single_Vispa2Matrix(tf)
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+                            df <- import_single_Vispa2Matrix(tf2)
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                         }
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                     )
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                 ),