Code updates to remove warnings; updated templates

ClevelandClinicQHS · Apr 24, 2021 · 6000468 · 6000468
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: projects
 Title: A Project Infrastructure for Researchers
-Version: 2.1.2
+Version: 2.1.3
 Authors@R: 
     c(person(given = "Nik",
              family = "Krieger",
@@ -40,8 +40,7 @@ Suggests:
     here (>= 0.1),
     testthat (>= 2.3.2)
 Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Collate: 
     'set_generics.R'
     'class-projects_author.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,11 @@
 
+# projects 2.1.3
+
+## Minor updates:
+- Removed names from arguments passed to `readr::write_lines()` and `readr::write_rds()` since they have deprecated `path` in favor of `file`.
+- Combined the `setup` and `load_libraries` code chunks in all applicable template .Rmd files.
+- Removed `LazyData` line from `DESCRIPTION` file in compliance with new CRAN check.
+
 # projects 2.1.2
 
 ## Minor updates:

diff --git a/R/file_management.R b/R/file_management.R
@@ -465,7 +465,7 @@ archive_project <- function(project) {
 
   projects_table$path[projects_table$id == project_row$id]   <- new_path
 
-  readr::write_rds(x = projects_table, path = projects_path)
+  readr::write_rds(projects_table, projects_path)
 
   print(dplyr::filter(projects_table, .data$id == project_row$id))
   message("\nThe above project was archived and has the file path\n", new_path)
@@ -640,7 +640,7 @@ move_projects_folder <- function(new_path,
       replacement = new_path
     )
 
-  readr::write_rds(projects_table, path = projects_path)
+  readr::write_rds(projects_table, projects_path)
 
   message("\nProjects folder moved so that its new path is\n", new_path2)
 }
@@ -699,7 +699,7 @@ rename_projects_folder <- function(new_name,
       replacement = new_path
     )
 
-  readr::write_rds(projects_table, path = projects_path)
+  readr::write_rds(projects_table, projects_path)
 
   message("\nProjects folder renamed so that its new path is:\n", new_path)
 }
diff --git a/R/metadata_manipulation.R b/R/metadata_manipulation.R
@@ -52,7 +52,7 @@ add_metadata <- function(table, new_row, table_path) {
 
   table <- vec_rbind(table, new_row)
 
-  readr::write_rds(x = table, path = table_path)
+  readr::write_rds(table, table_path)
 
   table[nrow(table), ]
 }
@@ -73,7 +73,7 @@ edit_metadata <- function(table, row_id, ..., table_path) {
     }
   )
 
-  readr::write_rds(x = table, path = table_path)
+  readr::write_rds(table, table_path)
 
   table[row_number, ]
 }
@@ -84,7 +84,7 @@ delete_metadata <- function(table, row_id, table_path) {
 
   table <- table[table$id != row_id, ]
 
-  readr::write_rds(x = table, path = table_path)
+  readr::write_rds(table, table_path)
 }
 
 
@@ -93,7 +93,7 @@ add_assoc <- function(assoc_table, new_rows, assoc_path) {
 
   assoc_table <- rbind(assoc_table, new_rows)
 
-  readr::write_rds(x = assoc_table, path = assoc_path)
+  readr::write_rds(assoc_table, assoc_path)
 
   assoc_table
 }
@@ -109,7 +109,7 @@ delete_assoc <- function(assoc_table, ..., assoc_path) {
       dplyr::anti_join(assoc_table, assoc_to_delete)
     )
 
-  readr::write_rds(x = assoc_table, path = assoc_path)
+  readr::write_rds(assoc_table, assoc_path)
 
   assoc_table
 }
@@ -125,7 +125,7 @@ change_special_author <- function(author_id,
     change_matrix <- projects_table[special_author_cols] == author_id
     if (isTRUE(any(change_matrix))) {
       projects_table[special_author_cols][change_matrix] <- new_value
-      readr::write_rds(x = projects_table, path = projects_path)
+      readr::write_rds(projects_table, projects_path)
     }
   }
 }

diff --git a/R/setup.R b/R/setup.R
@@ -227,7 +227,7 @@ set_Renviron <- function(projects_folder_path, .Renviron_path) {
       )
     )
 
-  readr::write_lines(Renviron_entries, path = .Renviron_path)
+  readr::write_lines(Renviron_entries, .Renviron_path)
   Sys.setenv(PROJECTS_FOLDER_PATH = projects_folder_path)
 }
 
@@ -360,7 +360,7 @@ restore_metadata <- function(path) {
         if (fs::file_exists(rds_path)) {
           tibble <- vec_rbind(readRDS(rds_path), tibble)
         }
-        readr::write_rds(x = tibble, path = rds_path)
+        readr::write_rds(tibble, rds_path)
       }
   )
 }

diff --git a/R/update.R b/R/update.R
@@ -102,7 +102,7 @@ update_metadata <- function(ask = TRUE) {
     projects_table$creator <- creator_results$results
   }
 
-  readr::write_rds(x = projects_table, path = projects_path)
+  readr::write_rds(projects_table, projects_path)
 
   message("\nProjects metadata updated.")
 

diff --git a/README.md b/README.md
@@ -378,7 +378,7 @@ library(projects)
 ``` r
 setup_projects("~")
 #> projects folder created at
-#> /tmp/RtmpBBoEOw/projects
+#> /tmp/RtmpH0SVxn/projects
 #> 
 #> Add affiliations with new_affiliation(),
 #> then add authors with new_author(),
@@ -579,7 +579,7 @@ new_project(
 )
 #> 
 #> Project 1 has been created at
-#> /tmp/RtmpBBoEOw/projects/p0001
+#> /tmp/RtmpH0SVxn/projects/p0001
 #> # A tibble: 1 x 6
 #>      id title             stage     status     deadline_type deadline           
 #>   <int> <chr>             <prjstg>  <chr>      <chr>         <dttm>             
@@ -620,7 +620,7 @@ new_project(
 )
 #> 
 #> Project 2 has been created at
-#> /tmp/RtmpBBoEOw/projects/p0002
+#> /tmp/RtmpH0SVxn/projects/p0002
 #> # A tibble: 1 x 6
 #>      id title          stage         status    deadline_type deadline           
 #>   <int> <chr>          <prjstg>      <chr>     <chr>         <dttm>             
@@ -653,7 +653,7 @@ new_project(
 )
 #> 
 #> Project 1945 has been created at
-#> /tmp/RtmpBBoEOw/projects/top_secret/p1945
+#> /tmp/RtmpH0SVxn/projects/top_secret/p1945
 #> # A tibble: 1 x 6
 #>      id title        stage           status    deadline_type deadline           
 #>   <int> <chr>        <prjstg>        <chr>     <chr>         <dttm>             
@@ -682,7 +682,7 @@ new_project(
 )
 #> 
 #> Project 3 has been created at
-#> /tmp/RtmpBBoEOw/projects/p0003
+#> /tmp/RtmpH0SVxn/projects/p0003
 #> # A tibble: 1 x 6
 #>      id title         stage       status       deadline_type deadline           
 #>   <int> <chr>         <prjstg>    <chr>        <chr>         <dttm>             
@@ -801,9 +801,9 @@ projects(verbose = TRUE) %>% select(id, short_title, path)
 #> # A tibble: 3 x 3
 #>      id short_title     path                                     
 #>   <int> <chr>           <chr>                                    
-#> 1  1945 Dr. Strangelove /tmp/RtmpBBoEOw/projects/top_secret/p1945
-#> 2     2 Eureka!         /tmp/RtmpBBoEOw/projects/p0002           
-#> 3     3 Rn86            /tmp/RtmpBBoEOw/projects/p0003
+#> 1  1945 Dr. Strangelove /tmp/RtmpH0SVxn/projects/top_secret/p1945
+#> 2     2 Eureka!         /tmp/RtmpH0SVxn/projects/p0002           
+#> 3     3 Rn86            /tmp/RtmpH0SVxn/projects/p0003
 ```
 
 Users can also create subdirectories with the function
@@ -813,7 +813,7 @@ Users can also create subdirectories with the function
 new_project_group("Greek_studies/ancient_studies")
 #> 
 #> The following directory was created:
-#> /tmp/RtmpBBoEOw/projects/Greek_studies/ancient_studies
+#> /tmp/RtmpH0SVxn/projects/Greek_studies/ancient_studies
 ```
 
 If a project has already been created, it can be moved **not** with
@@ -833,7 +833,7 @@ move_project("Crown", path = "Greek_studies/ancient_studies")
 #> #   creator <prjaut>
 #> 
 #> Project 2 moved so that its new path is
-#> /tmp/RtmpBBoEOw/projects/Greek_studies/ancient_studies/p0002
+#> /tmp/RtmpH0SVxn/projects/Greek_studies/ancient_studies/p0002
 
 copy_project(
   project_to_copy = "Radon",
@@ -848,7 +848,7 @@ copy_project(
 #> #   creator <prjaut>
 #> 
 #> Project 4 below is a copy of project 3 and is located at
-#> /tmp/RtmpBBoEOw/projects/dangerous_studies/radioactive_studies/radon_studies/p0004
+#> /tmp/RtmpH0SVxn/projects/dangerous_studies/radioactive_studies/radon_studies/p0004
 #> # A tibble: 1 x 11
 #>      id title short_title current_owner status deadline_type deadline           
 #>   <int> <chr> <lgl>       <prjaut>      <chr>  <chr>         <dttm>             
@@ -857,9 +857,9 @@ copy_project(
 #> #   creator <prjaut>
 #> 
 #> The .Rproj file
-#> /tmp/RtmpBBoEOw/projects/dangerous_studies/radioactive_studies/radon_studies/p0004/p0003.Rproj
+#> /tmp/RtmpH0SVxn/projects/dangerous_studies/radioactive_studies/radon_studies/p0004/p0003.Rproj
 #> was renamed to
-#> /tmp/RtmpBBoEOw/projects/dangerous_studies/radioactive_studies/radon_studies/p0004/p0004.Rproj
+#> /tmp/RtmpH0SVxn/projects/dangerous_studies/radioactive_studies/radon_studies/p0004/p0004.Rproj
 #> 
 #> Be sure to change all instances of "p0003" to "p0004" as desired
 #> (e.g., .bib files and references to them in YAML headers).
@@ -870,9 +870,9 @@ projects(c("Crown", "Radon"), verbose = TRUE) %>% select(id, title, path)
 #> # A tibble: 3 x 3
 #>      id title           path                                                    
 #>   <int> <chr>           <chr>                                                   
-#> 1     2 Weighing the C… /tmp/RtmpBBoEOw/projects/Greek_studies/ancient_studies/…
-#> 2     4 Understanding … /tmp/RtmpBBoEOw/projects/dangerous_studies/radioactive_…
-#> 3     3 Understanding … /tmp/RtmpBBoEOw/projects/p0003
+#> 1     2 Weighing the C… /tmp/RtmpH0SVxn/projects/Greek_studies/ancient_studies/…
+#> 2     4 Understanding … /tmp/RtmpH0SVxn/projects/dangerous_studies/radioactive_…
+#> 3     3 Understanding … /tmp/RtmpH0SVxn/projects/p0003
 ```
 
 Projects can also be archived; they are moved into a subdirectory called
@@ -890,7 +890,7 @@ archive_project("Strangelove")
 #> #   creator <prjaut>
 #> 
 #> The above project was archived and has the file path
-#> /tmp/RtmpBBoEOw/projects/top_secret/archive/p1945
+#> /tmp/RtmpH0SVxn/projects/top_secret/archive/p1945
 ```
 
 When a project is archived, it is no longer included in `projects()`
@@ -901,18 +901,18 @@ projects(verbose = TRUE) %>% select(id, short_title, path)
 #> # A tibble: 3 x 3
 #>      id short_title path                                                        
 #>   <int> <chr>       <chr>                                                       
-#> 1     2 Eureka!     /tmp/RtmpBBoEOw/projects/Greek_studies/ancient_studies/p0002
-#> 2     4 <NA>        /tmp/RtmpBBoEOw/projects/dangerous_studies/radioactive_stud…
-#> 3     3 Rn86        /tmp/RtmpBBoEOw/projects/p0003
+#> 1     2 Eureka!     /tmp/RtmpH0SVxn/projects/Greek_studies/ancient_studies/p0002
+#> 2     4 <NA>        /tmp/RtmpH0SVxn/projects/dangerous_studies/radioactive_stud…
+#> 3     3 Rn86        /tmp/RtmpH0SVxn/projects/p0003
 
 projects(verbose = TRUE, archived = TRUE) %>% select(id, short_title, path)
 #> # A tibble: 4 x 3
 #>      id short_title    path                                                     
 #>   <int> <chr>          <chr>                                                    
-#> 1  1945 Dr. Strangelo… /tmp/RtmpBBoEOw/projects/top_secret/archive/p1945        
-#> 2     2 Eureka!        /tmp/RtmpBBoEOw/projects/Greek_studies/ancient_studies/p…
-#> 3     4 <NA>           /tmp/RtmpBBoEOw/projects/dangerous_studies/radioactive_s…
-#> 4     3 Rn86           /tmp/RtmpBBoEOw/projects/p0003
+#> 1  1945 Dr. Strangelo… /tmp/RtmpH0SVxn/projects/top_secret/archive/p1945        
+#> 2     2 Eureka!        /tmp/RtmpH0SVxn/projects/Greek_studies/ancient_studies/p…
+#> 3     4 <NA>           /tmp/RtmpH0SVxn/projects/dangerous_studies/radioactive_s…
+#> 4     3 Rn86           /tmp/RtmpH0SVxn/projects/p0003
 ```
 
 Lastly, affiliations, authors and projects can be deleted with the
@@ -974,7 +974,7 @@ various stages of development.
 
 # References
 
-<div id="refs" class="references hanging-indent">
+<div id="refs" class="references">
 
 <div id="ref-baker20161">
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,4 +1,9 @@
 
+## Update to version 2.1.3
+There were no ERRORs, WARNINGs.
+
+NOTE on some platforms objecting to `methods` being in the `Imports` list.
+
 ## Update to version 2.1.2
 There were no ERRORs, WARNINGs.
 

diff --git a/inst/templates/04_report.Rmd b/inst/templates/04_report.Rmd
@@ -13,9 +13,7 @@ Funding:
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE)
-```
 
-```{r load_libraries, include=FALSE}
 library(projects)
 library(here)
 library(tidyverse)

diff --git a/inst/templates/CONSORT_protocol.Rmd b/inst/templates/CONSORT_protocol.Rmd
@@ -15,10 +15,7 @@ Funding:
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE)
-```
-
 
-```{r load_libraries, include=FALSE}
 library(projects)
 library(here)
 library(tidyverse)

diff --git a/inst/templates/STROBE_protocol.Rmd b/inst/templates/STROBE_protocol.Rmd
@@ -15,10 +15,7 @@ Funding:
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE)
-```
-
 
-```{r load_libraries, include=FALSE}
 library(projects)
 library(here)
 library(tidyverse)