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$cleanup(force = FALSE)
Arguments
primary_path
: Path of the primary, user level cache. Defaults to the user level cache directory of the machine.replica_path
: Path of the replica. Defaults to a temporary directory within the session temporary directory.platforms
: seedefault_platforms()
for possible values.r_version
: R version to create the cache for.bioc
: Whether to include BioConductor packages.cran_mirror
: CRAN mirror to use, this takes precedence overrepos
.repos
: Repositories to use.update_after
:difftime
object. Automatically update the cache if it gets older than this. Set it toInf
to avoid updates. Defaults to seven days.packages
: Packages to query, character vector.dependencies
: Which kind of dependencies to include. Works the same way as thedependencies
argument ofutils::install.packages()
.recursive
: Whether to include recursive dependencies.force
: Whether to force cleanup without asking the user.
Details
cranlike_metadata_cache$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 fromDESCRIPTION
, orNA_character_
.suggests
:Suggests
field fromDESCRIPTION
, orNA_character_
.built
:Built
field fromDESCIPTION
, if a binary package, orNA_character_
.imports
:Imports
field fromDESCRIPTION
, orNA_character_
.archs
:Archs
entries fromPACKAGES
files. Might be missing.repodir
: The directory of the file, inside the repository.platform
: This is a character vector. Seedefault_platforms()
for more about platform names. In practice each value of theplatform
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
orcran
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 theArchive
directory as well, in case the package has been archived since the metadata was cached.filesize
: Size of the file, if known, in bytes, orNA_integer_
.sha256
: The SHA256 hash of the file, if known, orNA_character_
.deps
: All package dependencies, in a data frame.license
: Package license, might beNA
for binary packages.linkingto
:LinkingTo
field fromDESCRIPTION
, orNA_character_
.enhances
:Enhances
field fromDESCRIPTION
, orNA_character_
.os_type
:unix
orwindows
for OS specific packages. UsuallyNA
.priority
: "optional", "recommended" orNA
. (Base packages are normally not included in the list, so "base" should not appear here.)md5sum
: MD5 sum, if available, may beNA
.sysreqs
: TheSystemRequirements
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: 5.07 MB in 4 files.
#>
#> ℹ Updating metadata database
#> ✔ Updating metadata database ... done
#>
#> # A data frame: 43,564 × 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 2.2.2 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 43,554 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 2.3.9 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 2.1.2 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 2.3.9 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>