diff --git a/.lintr b/.lintr index 0c778269..b008c93b 100644 --- a/.lintr +++ b/.lintr @@ -4,4 +4,4 @@ linters: linters_with_defaults( object_usage_linter = NULL, cyclocomp_linter = NULL ) -exclusions: list("tests/testthat.R", "R/cpp11.R") +exclusions: list("tests/testthat.R", "R/cpp11.R", "R/import-standalone-utils-assert.R", "R/import-standalone-utils-assert-path.R") diff --git a/vignettes/collaboration.Rmd b/vignettes/collaboration.Rmd index 50f7cf2d..e5d9c1a4 100644 --- a/vignettes/collaboration.Rmd +++ b/vignettes/collaboration.Rmd @@ -233,7 +233,7 @@ This multi-step process means that we avoid copying data that is already known a It is important that the `.outpack` directory is *not* shared via git; we warn about this now, and you can use `orderly2::ordery_gitignore_update()` to automatically create a suitable `.gitignore` file that will prevent it being accidentally committed. -However, +However, If Alice and Bob were starting on a new machine they would: @@ -253,20 +253,20 @@ One of the simplest ways to share packets with a collaborator is through a share 1. Initialise an orderly location on the shared file system ```{r as="alice"} orderly2::orderly_init( - root = path_sharepoint_alice, - path_archive = NULL, - use_file_store = TRUE, + root = path_sharepoint_alice, + path_archive = NULL, + use_file_store = TRUE, require_complete_tree = TRUE ) ``` - + Create an orderly store with a file store and a complete tree. See `orderly2::orderly_init()` for more details. 1. Add this as a location ```{r, as="alice", inwd = path_alice} orderly2::orderly_location_add( "sharepoint", "path", list(path = path_sharepoint_alice)) ``` - + 1. Push any packets you want to share ```{r, as="alice", inwd = path_alice} orderly2::orderly_location_push(id, "sharepoint") @@ -280,11 +280,10 @@ Then these will be available for your collaborator to pull. Note that the data i orderly2::orderly_location_add( "alices_orderly", "path", list(path = path_sharepoint_bob)) ``` - + 1. Pull the metadata and use the packets as desired ```{r, as="bob", inwd = path_bob} orderly2::orderly_location_pull_metadata( "alices_orderly" ) ``` - diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd index 5b8634cd..6902440e 100644 --- a/vignettes/introduction.Rmd +++ b/vignettes/introduction.Rmd @@ -187,7 +187,8 @@ In addition, there is also a function `orderly::orderly_run_info()` that can be Let's add some additional annotations to the previous reports: ```{r, include = FALSE} -code_data <- readLines(file.path(path, "src", "incoming_data", "incoming_data.R")) +code_data <- readLines( + file.path(path, "src", "incoming_data", "incoming_data.R")) writeLines(c( "orderly2::orderly_strict_mode()", 'orderly2::orderly_resource("data.csv")',