Curate File Collections

Ideally, file collections are generated by passing proper file specifications in a single call to collate(). In reality, post-processing of the file collection objects is sometimes needed. Thus, we support a selected number of file collection operations.

Merge file collections

You can merge file collections after they are collated. This operation returns the union of the files.

library("pkglite")
pkg <- system.file("examples/pkg1/", package = "pkglite")

fc <- merge(
  pkg %>% collate(file_root_core()),
  pkg %>% collate(file_r()),
  pkg %>% collate(file_r(), file_man())
)

fc
#> -- File collection -------------------------------------------------------------
#> -- Package: pkg1 ---------------------------------------------------------------
#>                path_rel format
#> 1           DESCRIPTION   text
#> 2             NAMESPACE   text
#> 3               NEWS.md   text
#> 4             README.md   text
#> 5              R/data.R   text
#> 6             R/hello.R   text
#> 7      R/pkg1-package.R   text
#> 8         R/sysdata.rda binary
#> 9        man/dataset.Rd   text
#> 10   man/hello_world.Rd   text
#> 11  man/pkg1-package.Rd   text
#> 12 man/figures/logo.png binary

By design, one file collection object only stores metadata of files from a single package. Therefore, merging file collections from different packages will result in an error.

Prune file collections

To remove files from a file collection, use prune():

fc %>% prune(path = c("NEWS.md", "man/figures/logo.png"))
#> -- File collection -------------------------------------------------------------
#> -- Package: pkg1 ---------------------------------------------------------------
#>               path_rel format
#> 1          DESCRIPTION   text
#> 2            NAMESPACE   text
#> 3            README.md   text
#> 4             R/data.R   text
#> 5            R/hello.R   text
#> 6     R/pkg1-package.R   text
#> 7        R/sysdata.rda binary
#> 8       man/dataset.Rd   text
#> 9   man/hello_world.Rd   text
#> 10 man/pkg1-package.Rd   text

Only the files matching the exact relative path(s) will be removed.

The prune operation is type-stable. If all files in a file collection are removed, an empty file collection is returned so that it can still be merged with the other file collections.

pkg %>%
  collate(file_data()) %>%
  prune(path = "data/dataset.rda")
#> -- File collection -------------------------------------------------------------
#> -- Package: pkg1 ---------------------------------------------------------------
#> [1] path_rel format  
#> <0 rows> (or 0-length row.names)

Sanitize file collections

A file collection might contain files that should almost always be excluded, such as the files defined in pattern_file_sanitize():

pattern_file_sanitize()
#> [1] "/\\.DS_Store$"     "/Thumbs\\.db$"     "/\\.git$"         
#> [4] "/\\.svn$"          "/\\.hg$"           "/\\.Rproj\\.user$"
#> [7] "/\\.Rhistory$"     "/\\.RData$"        "/\\.Ruserdata$"

You can use sanitize() to remove such files (if any) from a file collection:

fc %>% sanitize()
#> -- File collection -------------------------------------------------------------
#> -- Package: pkg1 ---------------------------------------------------------------
#>                path_rel format
#> 1           DESCRIPTION   text
#> 2             NAMESPACE   text
#> 3               NEWS.md   text
#> 4             README.md   text
#> 5              R/data.R   text
#> 6             R/hello.R   text
#> 7      R/pkg1-package.R   text
#> 8         R/sysdata.rda binary
#> 9        man/dataset.Rd   text
#> 10   man/hello_world.Rd   text
#> 11  man/pkg1-package.Rd   text
#> 12 man/figures/logo.png binary