R: Cache for package data and metadata

pkgcache-package {pkgcache}

R Documentation

Cache for package data and metadata

Description

Metadata and package cache for CRAN-like repositories. This is a utility package to be used by package management tools that want to take advantage of caching.

Details

Metadata and package cache for CRAN-like repositories. This is a utility package to be used by package management tools that want to take advantage of caching.

Installation

You can install the released version of pkgcache from CRAN with:

install.packages("pkgcache")

If you need the development version, you can install it from GitHub with:

pak::pak("r-lib/pkgcache")

Metadata cache

meta_cache_list() lists all packages in the metadata cache. It includes Bioconductor package, and all versions (i.e. both binary and source) of the packages for the current platform and R version.

(We load the pillar package, because it makes the pkgcache data frames print nicer, similarly to tibbles.)

library(pkgcache)
library(pillar)
meta_cache_list()
#> # A data frame: 44,780 x 32
#>    package     version depends suggests license imports linkingto archs enhances
#>    <chr>       <chr>   <chr>   <chr>    <chr>   <chr>   <chr>     <chr> <chr>   
#>  1 A3          1.0.0   R (>= ~ randomF~ GPL (>~ <NA>    <NA>      <NA>  <NA>    
#>  2 AATtools    0.0.2   R (>= ~ <NA>     GPL-3   magrit~ <NA>      <NA>  <NA>    
#>  3 ABACUS      1.0.0   R (>= ~ rmarkdo~ GPL-3   ggplot~ <NA>      <NA>  <NA>    
#>  4 ABC.RAP     0.9.0   R (>= ~ knitr, ~ GPL-3   graphi~ <NA>      <NA>  <NA>    
#>  5 ABCanalysis 1.2.1   R (>= ~ <NA>     GPL-3   plotrix <NA>      <NA>  <NA>    
#>  6 ABCoptim    0.15.0  <NA>    testtha~ MIT + ~ Rcpp, ~ Rcpp      ABCo~ <NA>    
#>  7 ABCp2       1.2     MASS    <NA>     GPL-2   <NA>    <NA>      <NA>  <NA>    
#>  8 ABHgenotyp~ 1.0.1   <NA>    knitr, ~ GPL-3   ggplot~ <NA>      <NA>  <NA>    
#>  9 ABM         0.3     <NA>    <NA>     GPL (>~ R6, Rc~ Rcpp      ABM.~ <NA>    
#> 10 ABPS        0.3     <NA>    testthat GPL (>~ kernlab <NA>      <NA>  <NA>    
#> # i 44,770 more rows
#> # i 23 more variables: license_restricts_use <chr>, priority <chr>,
#> #   license_is_foss <chr>, os_type <chr>, repodir <chr>, rversion <chr>,
#> #   platform <chr>, needscompilation <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>, path <chr>

meta_cache_deps() and meta_cache_revdeps() can be used to look up dependencies and reverse dependencies.

The metadata is updated automatically if it is older than seven days, and it can also be updated manually with meta_cache_update().

See the cranlike_metadata_cache R6 class for a lower level API, and more control.

Package cache

Package management tools may use the ⁠pkg_cache_*⁠ functions and in particular the package_cache class, to make use of local caching of package files.

The ⁠pkg_cache_*⁠ API is high level, and uses a user level cache:

pkg_cache_summary()
#> $cachepath
#> [1] "/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/pkg"
#> 
#> $files
#> [1] 176
#> 
#> $size
#> [1] 204562277

pkg_cache_list()
#> # A data frame: 176 x 11
#>    fullpath    path  package url   etag  sha256 version platform built vignettes
#>    <chr>       <chr> <chr>   <chr> <chr> <chr>  <chr>   <chr>    <int>     <int>
#>  1 /Users/gab~ bin/~ diffvi~ http~ "\"2~ e8869~ 0.1.1   aarch64~    NA        NA
#>  2 /Users/gab~ src/~ testth~ <NA>   <NA> <NA>   0.0.0.~ source       1         0
#>  3 /Users/gab~ src/~ testth~ <NA>   <NA> <NA>   0.0.0.~ aarch64~     1         0
#>  4 /Users/gab~ bin/~ DT      http~ "\"1~ 69c62~ 0.27    aarch64~    NA        NA
#>  5 /Users/gab~ bin/~ R6      http~ "\"1~ 00398~ 2.5.1   aarch64~    NA        NA
#>  6 /Users/gab~ src/~ cli     <NA>   <NA> c37f3~ 3.6.1.~ source       1         0
#>  7 /Users/gab~ src/~ cli     <NA>   <NA> c37f3~ 3.6.1.~ aarch64~     1         0
#>  8 /Users/gab~ bin/~ glue    http~ "\"2~ 25019~ 1.6.2   aarch64~    NA        NA
#>  9 /Users/gab~ src/~ cli     <NA>   <NA> f6794~ 3.1.0.~ source       1         0
#> 10 /Users/gab~ src/~ cli     <NA>   <NA> f6794~ 3.1.0.~ aarch64~     1         0
#> # i 166 more rows
#> # i 1 more variable: rversion <chr>

pkg_cache_find(package = "dplyr")
#> # A data frame: 1 x 11
#>   fullpath     path  package url   etag  sha256 version platform built vignettes
#>   <chr>        <chr> <chr>   <chr> <chr> <chr>  <chr>   <chr>    <int>     <int>
#> 1 /Users/gabo~ bin/~ dplyr   http~ "\"1~ cb4f7~ 1.1.2   aarch64~    NA        NA
#> # i 1 more variable: rversion <chr>

pkg_cache_add_file() can be used to add a file, pkg_cache_delete_files() to remove files, pkg_cache_get_files() to copy files out of the cache.

The package_cache class provides a finer API.

Installed packages

pkgcache contains a very fast DCF parser to parse ⁠PACKAGES*⁠ files, or the DESCRIPTION files in installed packages. parse_packages() parses all fields from PACKAGES, PACKAGES.gz or PACKAGES.rds files. parse_installed() reads all metadata from packages installed into a library:

parse_installed()
#> # A data frame: 329 x 97
#>    Package     Type  Title Version Date  Author Maintainer Description Copyright
#>    <chr>       <chr> <chr> <chr>   <chr> <chr>  <chr>      <chr>       <chr>    
#>  1 AsioHeaders Pack~ "'As~ 1.22.1~ 2022~ "Dirk~ Dirk Edde~ "'Asio' is~ file ins~
#>  2 BiocGeneri~ <NA>  "S4 ~ 0.46.0  <NA>  "The ~ Hervé Pag~ "The packa~ <NA>     
#>  3 BiocManager <NA>  "Acc~ 1.30.20 <NA>  "Mart~ Marcel Ra~ "A conveni~ <NA>     
#>  4 Biostrings  <NA>  "Eff~ 2.67.2  <NA>  "Herv~ Hervé Pag~ "Memory ef~ <NA>     
#>  5 DBI         <NA>  "R D~ 1.1.3   2022~ "R Sp~ Kirill Mü~ "A databas~ <NA>     
#>  6 DBItest     <NA>  "Tes~ 1.7.3   2022~ "Kiri~ Kirill Mü~ "A helper ~ <NA>     
#>  7 DT          Pack~ "A W~ 0.27    <NA>  "Yihu~ Yihui Xie~ "Data obje~ <NA>     
#>  8 Distributi~ <NA>  "Dis~ 0.6-0   2018~ "Davi~ David Sco~ "Utilities~ <NA>     
#>  9 Formula     <NA>  "Ext~ 1.2-5   2023~ "Achi~ Achim Zei~ "Infrastru~ <NA>     
#> 10 GenomeInfo~ <NA>  "Uti~ 1.35.17 <NA>  "Sona~ Hervé Pag~ "Contains ~ <NA>     
#> # i 319 more rows
#> # i 88 more variables: License <chr>, URL <chr>, BugReports <chr>,
#> #   NeedsCompilation <chr>, Packaged <chr>, Repository <chr>,
#> #   `Date/Publication` <chr>, Built <chr>, biocViews <chr>, Encoding <chr>,
#> #   Depends <chr>, Imports <chr>, Suggests <chr>, Collate <chr>, git_url <chr>,
#> #   git_branch <chr>, git_last_commit <chr>, git_last_commit_date <chr>,
#> #   `Authors@R` <chr>, VignetteBuilder <chr>, RoxygenNote <chr>, ...

Bioconductor support

Both the metadata cache and the package cache support Bioconductor by default, automatically. See the BioC_mirror option and the R_BIOC_MIRROR and R_BIOC_VERSION environment variables below to configure Bioconductor support.

Package Options

The BioC_mirror option can be used to select a Bioconductor mirror. This takes priority over the R_BIOC_MIRROR environment variable.
You can use the pkg.current_platform option to set the platform string for the current platform for the current_r_platform() function. This is useful if pkgcache didn’t detect the platform correctly. Alternatively, you can use the PKG_CURRENT_PLATFORM environment variable. The option takes priority.
pkgcache_timeout is the HTTP timeout for all downloads. It is in seconds, and the limit for downloading the whole file. Defaults to 3600, one hour. It corresponds to the TIMEOUT libcurl option.
pkgcache_connecttimeout is the HTTP timeout for the connection phase. It is in seconds and defaults to 30 seconds. It corresponds to the CONNECTTIMEOUT libcurl option.
pkgcache_low_speed_limit and pkgcache_low_speed_time are used for a more sensible HTTP timeout. If the download speed is less than pkgcache_low_speed_limit bytes per second for at least pkgcache_low_speed_time seconds, the download errors. They correspond to the LOW_SPEED_LIMIT and LOW_SPEED_TIME curl options.

Package environment variables

The R_BIOC_VERSION environment variable can be used to override the default Bioconductor version detection and force a given version. E.g. this can be used to force the development version of Bioconductor.
The R_BIOC_MIRROR environment variable can be used to select a Bioconductor mirror. The BioC_mirror option takes priority over this, if set.
You can use the PKG_CURRENT_PLATFORM environment variable to set the platform string for the current platform for the current_r_platform() function. This is useful if pkgcache didn’t detect the platform correctly. Alternatively, you can use the pkg.current_platofrm option, which takes. priority over the environment variable.
PKGCACHE_PPM_REPO is the name of the Posit Package Manager repository to use. Defaults to "cran".
PKGCACHE_PPM_URL is the base URL of the Posit Package Manager instance to use. It defaults to the URL of the Posit Public Package Manager instance at https://packagemanager.posit.co/client/#/.
PKGCACHE_TIMEOUT is the HTTP timeout for all downloads. It is in seconds, and the limit for downloading the whole file. Defaults to 3600, one hour. It corresponds to the TIMEOUT libcurl option. The pkgcache_timeout option has priority over this, if set.
PKGCACHE_CONNECTTIMEOUT is the HTTP timeout for the connection phase. It is in seconds and defaults to 30 seconds. It corresponds to the CONNECTTIMEOUT libcurl option. The pkgcache_connecttimeout option takes precedence over this, if set.
PKGCACHE_LOW_SPEED_LIMIT and PKGCACHE_LOW_SPEED_TIME are used for a more sensible HTTP timeout. If the download speed is less than PKGCACHE_LOW_SPEED_LIMIT bytes per second for at least PKGCACHE_LOW_SPEED_TIME seconds, the download errors. They correspond to the LOW_SPEED_LIMIT and LOW_SPEED_TIME curl options. The pkgcache_low_speed_time and pkgcache_low_speed_limit options have priority over these environment variables, if they are set.
R_PKG_CACHE_DIR is used for the cache directory, if set. (Otherwise tools::R_user_dir("pkgcache", "cache") is used, see also meta_cache_summary() and pkg_cache_summary()).

Using pkgcache in CRAN packages

If you use pkgcache in your CRAN package, please make sure that

you don’t use pkgcache in your examples, and
you set the R_USER_CACHE_DIR environment variable to a temporary directory (e.g. via tempfile()) during test cases. See the tests/testthat/setup.R file in pkgcache for an example.

This is to make sure that pkgcache does not modify the user’s files while running ⁠R CMD check⁠.

Code of Conduct

Please note that the pkgcache project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

MIT (c) Posit Software, PBC

Author(s)

Maintainer: Gábor Csárdi csardi.gabor@gmail.com

Other contributors:

Posit Software, PBC [copyright holder, funder]