pkgcache

Cache CRAN-like metadata and package files

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")

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: 42,012 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    0.0.1   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 ABPS        0.3     <NA>    testthat GPL (>~ kernlab <NA>      <NA>  <NA>    
#> 10 ACA         1.1     R (>= ~ <NA>     GPL     graphi~ <NA>      <NA>  <NA>    
#> # ... with 42,002 more rows, and 23 more variables: os_type <chr>,
#> #   priority <chr>, license_is_foss <chr>, license_restricts_use <chr>,
#> #   repodir <chr>, rversion <chr>, platform <chr>, needscompilation <chr>,
#> #   ref <chr>, type <chr>, direct <lgl>, status <chr>, target <chr>,
#> #   mirror <chr>, sources <list>, filesize <dbl>, 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] 413
#> 
#> $size
#> [1] 3493123806

pkg_cache_list()
#> # A data frame: 413 x 11
#>    fullpath    path  package url   etag  sha256 version platform built vignettes
#>    <chr>       <chr> <chr>   <chr> <chr> <chr>  <chr>   <chr>    <chr> <chr>    
#>  1 /Users/gab~ src/~ pak     file~  <NA> 4e451~ 0.2.0.~ source   <NA>  <NA>     
#>  2 /Users/gab~ src/~ pak     <NA>   <NA> <NA>   0.2.0.~ aarch64~ TRUE  FALSE    
#>  3 /Users/gab~ bin/~ cli     http~ "\"1~ cbf6f~ 3.1.1   aarch64~ <NA>  <NA>     
#>  4 /Users/gab~ src/~ R7      <NA>   <NA> 76af5~ <NA>    <NA>     FALSE <NA>     
#>  5 /Users/gab~ src/~ Annota~ http~ "\"4~ 9c18b~ 1.18.0  source   <NA>  <NA>     
#>  6 /Users/gab~ bin/~ GGally  http~ "\"1~ a8ab8~ 2.1.2   aarch64~ <NA>  <NA>     
#>  7 /Users/gab~ src/~ ensemb~ http~ "\"3~ 0913f~ 2.18.3  source   <NA>  <NA>     
#>  8 /Users/gab~ src/~ bioviz~ http~ "\"2~ 5faa6~ 1.42.0  source   <NA>  <NA>     
#>  9 /Users/gab~ src/~ Annota~ http~ "\"4~ 283e2~ 1.56.2  source   <NA>  <NA>     
#> 10 /Users/gab~ src/~ rtrack~ http~ "\"3~ 0c5e4~ 1.54.0  source   <NA>  <NA>     
#> # ... with 403 more rows, and 1 more variable: rversion <chr>

pkg_cache_find(package = "dplyr")
#> # A data frame: 3 x 11
#>   fullpath     path  package url   etag  sha256 version platform built vignettes
#>   <chr>        <chr> <chr>   <chr> <chr> <chr>  <chr>   <chr>    <chr> <chr>    
#> 1 /Users/gabo~ src/~ dplyr   http~ "\"d~ 3b6aa~ 1.0.8   source   <NA>  <NA>     
#> 2 /Users/gabo~ bin/~ dplyr   http~ "\"6~ e46b3~ 1.0.7   aarch64~ <NA>  <NA>     
#> 3 /Users/gabo~ bin/~ dplyr   http~ "\"1~ 94913~ 1.0.8   aarch64~ <NA>  <NA>     
#> # ... with 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.

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.
• 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.
• 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 rappdirs::user_cache_dir() 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) RStudio Inc