Metadata cache for a CRAN-like repository — cranlike_metadata

This is an R6 class that implements the metadata cache of a CRAN-like repository. For a higher level interface, see the meta_cache_list(), meta_cache_deps(), meta_cache_revdeps() and meta_cache_update() functions.

Details

The cache has several layers:

The data is stored inside the cranlike_metadata_cache object.
It is also stored as an RDS file, in the session temporary directory. This ensures that the same data is used for all queries of a cranlike_metadata_cache object.
It is stored in an RDS file in the user's cache directory.
The downloaded raw PACKAGES* files are cached, together with HTTP ETags, to minimize downloads.

It has a synchronous and an asynchronous API.

Usage

cmc <- cranlike_metadata_cache$new(
  primary_path = NULL, replica_path = tempfile(),
  platforms = default_platforms(), r_version = getRversion(),
  bioc = TRUE, cran_mirror = default_cran_mirror(),
  repos = getOption("repos"),
  update_after = as.difftime(7, units = "days"))

cmc$list(packages = NULL)
cmc$async_list(packages = NULL)

cmc$deps(packages, dependencies = NA, recursive = TRUE)
cmc$async_deps(packages, dependencies = NA, recursive = TRUE)

cmc$revdeps(packages, dependencies = NA, recursive = TRUE)
cmc$async_revdeps(packages, dependencies = NA, recursive = TRUE)

cmc$update()
cmc$async_update()
cmc$check_update()
cmc$asnyc_check_update()

cmc$summary()

cmc$cleanup(force = FALSE)

Arguments

primary_path: Path of the primary, user level cache. Defaults to the user level cache directory of the machine.
replica_path: Path of the replica. Defaults to a temporary directory within the session temporary directory.
platforms: see default_platforms() for possible values.
r_version: R version to create the cache for.
bioc: Whether to include BioConductor packages.
cran_mirror: CRAN mirror to use, this takes precedence over repos.
repos: Repositories to use.
update_after: difftime object. Automatically update the cache if it gets older than this. Set it to Inf to avoid updates. Defaults to seven days.
packages: Packages to query, character vector.
dependencies: Which kind of dependencies to include. Works the same way as the dependencies argument of utils::install.packages().
recursive: Whether to include recursive dependencies.
force: Whether to force cleanup without asking the user.

Details

cranlike_metadata_cache$new() creates a new cache object. Creation does not trigger the population of the cache. It is only populated on demand, when queries are executed against it. In your package, you may want to create a cache instance in the .onLoad() function of the package, and store it in the package namespace. As this is a cheap operation, the package will still load fast, and then the package code can refer to the common cache object.

cmc$list() lists all (or the specified) packages in the cache. It returns a data frame, see the list of columns below.

cmc$async_list() is similar, but it is asynchronous, it returns a deferred object.

cmc$deps() returns a data frame, with the (potentially recursive) dependencies of packages.

cmc$async_deps() is the same, but it is asynchronous, it returns a deferred object.

cmc$revdeps() returns a data frame, with the (potentially recursive) reverse dependencies of packages.

cmc$async_revdeps() does the same, asynchronously, it returns an deferred object.

cmc$update() updates the the metadata (as needed) in the cache, and then returns a data frame with all packages, invisibly.

cmc$async_update() is similar, but it is asynchronous.

cmc$check_update() checks if the metadata is current, and if it is not, it updates it.

cmc$async_check_update() is similar, but it is asynchronous.

cmc$summary() lists metadata about the cache, including its location and size.

cmc$cleanup() deletes the cache files from the disk, and also from memory.

Columns

The metadata data frame contains all available versions (i.e. sources and binaries) for all packages. It usually has the following columns, some might be missing on some platforms.

package: Package name.
title: Package title.
version: Package version.
depends: Depends field from DESCRIPTION, or NA_character_.
suggests: Suggests field from DESCRIPTION, or NA_character_.
built: Built field from DESCIPTION, if a binary package, or NA_character_.
imports: Imports field from DESCRIPTION, or NA_character_.
archs: Archs entries from PACKAGES files. Might be missing.
repodir: The directory of the file, inside the repository.
platform: This is a character vector. See default_platforms() for more about platform names. In practice each value of the platform column is either
- "source" for source packages,
- a platform string, e.g. x86_64-apple-darwin17.0 for macOS packages compatible with macOS High Sierra or newer.
needscompilation: Whether the package needs compilation.
type: bioc or cran currently.
target: The path of the package file inside the repository.
mirror: URL of the CRAN/BioC mirror.
sources: List column with URLs to one or more possible locations of the package file. For source CRAN packages, it contains URLs to the Archive directory as well, in case the package has been archived since the metadata was cached.
filesize: Size of the file, if known, in bytes, or NA_integer_.
sha256: The SHA256 hash of the file, if known, or NA_character_.
deps: All package dependencies, in a data frame.
license: Package license, might be NA for binary packages.
linkingto: LinkingTo field from DESCRIPTION, or NA_character_.
enhances: Enhances field from DESCRIPTION, or NA_character_.
os_type: unix or windows for OS specific packages. Usually NA.
priority: "optional", "recommended" or NA. (Base packages are normally not included in the list, so "base" should not appear here.)
md5sum: MD5 sum, if available, may be NA.
sysreqs: The SystemRequirements field, if available. This lists the required system libraries or other software for the package. This is usually available for CRAN and Bioconductor package and when it is explicitly available in the repository metadata.
published: The time the package was published at, in GMT, POSIXct class.

The data frame contains some extra columns as well, these are for internal use only.

Examples

dir.create(cache_path <- tempfile())
cmc <- cranlike_metadata_cache$new(cache_path, bioc = FALSE)
cmc$list()
#> 
#> ✔ Updated metadata database: 5.03 MB in 4 files.
#> 
#> ℹ Updating metadata database
#> ✔ Updating metadata database ... done
#> 
#> # A data frame: 43,266 × 32
#>    package       version depends suggests needscompilation license imports
#>    <chr>         <chr>   <chr>   <chr>    <chr>            <chr>   <chr>  
#>  1 A3            1.0.0   R (>= … randomF… NA               GPL (>… NA     
#>  2 AalenJohansen 1.0     NA      knitr, … NA               GPL (>… NA     
#>  3 AATtools      0.0.3   R (>= … NA       NA               GPL-3   magrit…
#>  4 ABACUS        1.0.0   R (>= … rmarkdo… NA               GPL-3   ggplot…
#>  5 abasequence   0.1.0   NA      NA       NA               GPL-3   NA     
#>  6 abbreviate    0.1     NA      testtha… NA               GPL-3   NA     
#>  7 abc           2.2.1   R (>= … NA       NA               GPL (>… NA     
#>  8 abc.data      1.1     R (>= … NA       NA               GPL (>… NA     
#>  9 ABC.RAP       0.9.0   R (>= … knitr, … NA               GPL-3   graphi…
#> 10 ABCanalysis   1.2.1   R (>= … NA       NA               GPL-3   plotrix
#> # ℹ 43,256 more rows
#> # ℹ 25 more variables: linkingto <chr>, enhances <chr>,
#> #   license_restricts_use <chr>, os_type <chr>, path <chr>,
#> #   priority <chr>, license_is_foss <chr>, archs <chr>, repodir <chr>,
#> #   rversion <chr>, platform <chr>, ref <chr>, type <chr>, direct <lgl>,
#> #   status <chr>, target <chr>, mirror <chr>, sources <list>,
#> #   filesize <int>, sha256 <chr>, sysreqs <chr>, built <chr>, …
cmc$list("pkgconfig")
#> # A data frame: 2 × 32
#>   package   version depends suggests      needscompilation license imports
#> * <chr>     <chr>   <chr>   <chr>         <chr>            <chr>   <chr>  
#> 1 pkgconfig 2.0.3   NA      covr, testth… NA               MIT + … utils  
#> 2 pkgconfig 2.0.3   NA      covr, testth… no               MIT + … utils  
#> # ℹ 25 more variables: linkingto <chr>, enhances <chr>,
#> #   license_restricts_use <chr>, os_type <chr>, path <chr>,
#> #   priority <chr>, license_is_foss <chr>, archs <chr>, repodir <chr>,
#> #   rversion <chr>, platform <chr>, ref <chr>, type <chr>, direct <lgl>,
#> #   status <chr>, target <chr>, mirror <chr>, sources <list>,
#> #   filesize <int>, sha256 <chr>, sysreqs <chr>, built <chr>,
#> #   published <dttm>, deps <list>, md5sum <chr>
cmc$deps("pkgconfig")
#> # A data frame: 2 × 32
#>   package   version depends suggests      needscompilation license imports
#> * <chr>     <chr>   <chr>   <chr>         <chr>            <chr>   <chr>  
#> 1 pkgconfig 2.0.3   NA      covr, testth… NA               MIT + … utils  
#> 2 pkgconfig 2.0.3   NA      covr, testth… no               MIT + … utils  
#> # ℹ 25 more variables: linkingto <chr>, enhances <chr>,
#> #   license_restricts_use <chr>, os_type <chr>, path <chr>,
#> #   priority <chr>, license_is_foss <chr>, archs <chr>, repodir <chr>,
#> #   rversion <chr>, platform <chr>, ref <chr>, type <chr>, direct <lgl>,
#> #   status <chr>, target <chr>, mirror <chr>, sources <list>,
#> #   filesize <int>, sha256 <chr>, sysreqs <chr>, built <chr>,
#> #   published <dttm>, deps <list>, md5sum <chr>
cmc$revdeps("pkgconfig", recursive = FALSE)
#> # A data frame: 18 × 32
#>    package   version depends     suggests needscompilation license imports
#>  * <chr>     <chr>   <chr>       <chr>    <chr>            <chr>   <chr>  
#>  1 agua      0.1.4   parsnip     "covr, … NA               MIT + … "cli, …
#>  2 biospear  1.0.2   R (>= 2.10…  NA      no               GPL-2   "cobs,…
#>  3 hms       1.1.3   NA          "crayon… NA               MIT + … "lifec…
#>  4 igraph    2.1.1   methods, R… "ape (>… NA               GPL (>… "cli, …
#>  5 jtools    2.3.0   R (>= 3.6.… "boot, … NA               GPL (>… "cli, …
#>  6 pkgconfig 2.0.3   NA          "covr, … NA               MIT + … "utils"
#>  7 RSQLite   2.3.7   R (>= 3.1.… "callr,… NA               LGPL (… "bit64…
#>  8 spbabel   0.6.0   R (>= 3.2.… "testth… NA               GPL-3   "dplyr…
#>  9 tibble    3.2.1   R (>= 3.4.… "bench,… NA               MIT + … "fansi…
#> 10 agua      0.1.4   parsnip     "covr, … no               MIT + … "cli, …
#> 11 biospear  1.0.2   R (>= 2.10…  NA      no               GPL-2   "cobs,…
#> 12 hms       1.1.3   NA          "crayon… no               MIT + … "lifec…
#> 13 igraph    2.1.1   methods, R… "ape (>… yes              GPL (>… "cli, …
#> 14 jtools    2.3.0   R (>= 3.6.… "boot, … no               GPL (>… "cli, …
#> 15 pkgconfig 2.0.3   NA          "covr, … no               MIT + … "utils"
#> 16 RSQLite   2.3.7   R (>= 3.1.… "callr,… yes              LGPL (… "bit64…
#> 17 spbabel   0.6.0   R (>= 3.2.… "testth… no               GPL-3   "dplyr…
#> 18 tibble    3.2.1   R (>= 3.4.… "bench,… yes              MIT + … "fansi…
#> # ℹ 25 more variables: linkingto <chr>, enhances <chr>,
#> #   license_restricts_use <chr>, os_type <chr>, path <chr>,
#> #   priority <chr>, license_is_foss <chr>, archs <chr>, repodir <chr>,
#> #   rversion <chr>, platform <chr>, ref <chr>, type <chr>, direct <lgl>,
#> #   status <chr>, target <chr>, mirror <chr>, sources <list>,
#> #   filesize <int>, sha256 <chr>, sysreqs <chr>, built <chr>,
#> #   published <dttm>, deps <list>, md5sum <chr>