pass R check

bcbio · Oct 25, 2024 · ec29522 · ec29522
1 parent d96ea74
commit ec29522
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Showing 13 changed files with 20 additions and 73 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,7 +22,8 @@ Imports:
     yaml,
     whisker,
     rlang,
-    stringr
+    stringr,
+    utils
 Suggests: 
     hues,
     ggprism,

diff --git a/NAMESPACE b/NAMESPACE
@@ -16,3 +16,5 @@ importFrom(grDevices,colorRampPalette)
 importFrom(magrittr,"%>%")
 importFrom(readr,read_csv)
 importFrom(stringr,str_replace_all)
+importFrom(utils,download.file)
+importFrom(utils,unzip)
diff --git a/R/bcbioR-package.R b/R/bcbioR-package.R
@@ -6,6 +6,8 @@
 #' @importFrom magrittr %>%
 #' @importFrom readr read_csv
 #' @importFrom stringr str_replace_all
+#' @importFrom utils download.file
+#' @importFrom utils unzip
 ## usethis namespace: end
 #' @import usethis
 #' @import fs

diff --git a/R/helpers.R b/R/helpers.R
@@ -193,15 +193,17 @@ copy_templates <- function(path, pipeline, org=NULL){
     parts = c("templates/spatial")
   }
   analysis_template <- fs::path_package(base, parts)
-  org_template <- fs::path_package(base, parts, "org", org)
 
   ui_info("Getting templates from {ui_value(analysis_template)}")
   # ls_files <- grep("org", list.files(analysis_template, full.names = TRUE),
   #                  value = TRUE, invert = TRUE)
   # ui_info("{ui_value(length(ls_files))} amount of files to copy")
   copy_files_in_folder(analysis_template, path)
-  ui_info("Getting templates from {ui_value(org_template)}")
-  copy_files_in_folder(org_template, path, is_org=TRUE)
+  if (!is.null(org)){
+    org_template <- fs::path_package(base, parts, "org", org)
+    ui_info("Getting templates from {ui_value(org_template)}")
+    copy_files_in_folder(org_template, path, is_org=TRUE)
+  }
 
   # check org folder is in there
   # search for param + _README.md

diff --git a/README.md b/README.md
@@ -47,7 +47,7 @@ bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")
 
 ### Discover more…
 
-Go to the vignette to know more `vignette("bcbioR_quick_start",package="bcbioR")`
+Go to the vignette to know more `vignette("bcbioR_quick_start", package="bcbioR")`
 
 ## How to Contribute
 

diff --git a/inst/templates/rnaseq/org/hcbc/README.md → .../templates/rnaseq/org/hcbc/hcbc_README.md b/inst/templates/rnaseq/org/hcbc/README.md → .../templates/rnaseq/org/hcbc/hcbc_README.md
diff --git a/inst/templates/singlecell/Integration/01-integration.R b/inst/templates/singlecell/Integration/01-integration.R
diff --git a/man/bcbio_templates.Rd b/man/bcbio_templates.Rd
diff --git a/man/cb_friendly_pal.Rd b/man/cb_friendly_pal.Rd
diff --git a/man/cb_friendly_palettes.Rd b/man/cb_friendly_palettes.Rd
diff --git a/man/scale_color_cb_friendly.Rd b/man/scale_color_cb_friendly.Rd
diff --git a/man/scale_fill_cb_friendly.Rd b/man/scale_fill_cb_friendly.Rd
diff --git a/vignettes/bcbioR_quick_start.Rmd b/vignettes/bcbioR_quick_start.Rmd
@@ -64,8 +64,7 @@ We support multiple analyses type:
 
 - RNAseq
 - scRNAseq
-- TEAseq
-- COSMX
+- ChipPseq
 
 To get the example code for any of them you can use a similar command:
-Original file line number
+Diff line change
@@ Expand Up / @@ -64,8 +64,7 @@ We support multiple analyses type: @@
     - RNAseq
     - scRNAseq
-    - TEAseq
-    - COSMX
+    - ChipPseq
     To get the example code for any of them you can use a similar command:
@@ Expand Down @@