From 61ecfeab99d752fc032abaec3d317f8dd8cd5f6d Mon Sep 17 00:00:00 2001 From: John Elizarraras Date: Tue, 25 Jun 2024 09:55:49 -0500 Subject: [PATCH] Remove getwd occurrences --- CRAN-SUBMISSION | 6 +++--- R/clinicalomicsdbR.R | 6 ++---- README.Rmd | 2 +- README.md | 2 +- 4 files changed, 7 insertions(+), 9 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index ea1d1a2..a4f00a9 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 1.0.4 -Date: 2024-06-18 18:58:59 UTC -SHA: 584cc5189e1e0674fdbb7b28fedda3b4de5a2d87 +Version: 1.0.5 +Date: 2024-06-24 15:36:09 UTC +SHA: 00cdb469de694c5f9742ef1cc9cbf2f293296775 diff --git a/R/clinicalomicsdbR.R b/R/clinicalomicsdbR.R index 560557a..3eb1b2c 100644 --- a/R/clinicalomicsdbR.R +++ b/R/clinicalomicsdbR.R @@ -78,8 +78,7 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list( #' @param output_dir Directory to download files to. #' @return unmodifed clinicalomicsdbR object download = function(output_dir) { - cidr <- getwd() - dir.create(file.path(cidr, output_dir), recursive = TRUE, showWarnings = FALSE) + dir.create(output_dir, recursive = TRUE, showWarnings = FALSE) for (study_id in self$study_list) { dl_url <- self$get_download_url(study_id) message(paste0("Downloading study ", study_id, " from ", dl_url)) @@ -94,8 +93,7 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list( #' @param output_dir Directory to download files to. #' @return unmodifed clinicalomicsdbR object download_from_id = function(study_id) { - cidr <- getwd() - dir.create(file.path(cidr, output_dir), recursive = TRUE, showWarnings = FALSE) + dir.create(output_dir, recursive = TRUE, showWarnings = FALSE) dl_url <- self$get_download_url(study_id) tryCatch( { diff --git a/README.Rmd b/README.Rmd index fbaafd9..fb3f24b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -50,7 +50,7 @@ See Examples below to see how to use. - `new()` - Create new clinicalomicsdbR object. Needed before any other function - `filter(drugs, cancers)` - filters studies matching provided - arugments. `drugs` is a list and can be individual drugs or + arguments. `drugs` is a list and can be individual drugs or combinations. See the ClinicalOmicsDB website for all options. `cancers` can contain multiple cancers. - `download(output_dir)` - downloads all studies from `filter()` into diff --git a/README.md b/README.md index 1dcfbad..08ae698 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ See Examples below to see how to use. - `new()` - Create new clinicalomicsdbR object. Needed before any other function - `filter(drugs, cancers)` - filters studies matching provided - arugments. `drugs` is a list and can be individual drugs or + arguments. `drugs` is a list and can be individual drugs or combinations. See the ClinicalOmicsDB website for all options. `cancers` can contain multiple cancers. - `download(output_dir)` - downloads all studies from `filter()` into