R Package Repositories - Local Mirrors

by Henrik Bengtsson

Usage

make ## same as 'make sync-all'
make debug
make summary
make sync-all
make sync-cran
make sync-bioconductor

CRAN

Calling

$ make sync-cran

will create/update a local CRAN package repository under cran/ (in the current directory) with the following structure:

$ tree -d cran/
cran/
└── src
    └── contrib
        ├── PACKAGES
        ├── PACKAGES.gz
        ├── PACKAGES.in
        ├── PACKAGES.rds
        ├── A3_1.0.0.tar.gz
        ├── abbyyR_0.5.1.tar.gz
		:
        └── zyp_0.10-1.tar.gz

Bioconductor

Calling

$ make sync-bioconductor

will create/update three local Bioconductor package repositories under bioconductor/$BIOC_VERSION/ (in the current directory), where $BIOC_VERSION is the Bioconductor version (as automatically queried from Bioconductor):

• BioCsoft: Bioconductor Software packages (bioconductor/$BIOC_VERSION/bioc)
• BioCann: Bioconductor Annotation Data packages (bioconductor/$BIOC_VERSION/data/annotation)
• BioCexp: Bioconductor Experimental Data packages (bioconductor/$BIOC_VERSION/data/experiment)

Example of tree structure:

$ tree -d bioconductor/$BIOC_VERSION/bioc
cran/
└── src
    └── contrib
        ├── PACKAGES
        ├── PACKAGES.gz
        ├── PACKAGES.in
        ├── PACKAGES.rds
        ├── a4_1.26.0.tar.gz
        ├── a4Base_1.26.0.tar.gz
		:
        └── zlibbioc_1.24.0.tar.gz

Statistics

As of 2017-11-09, the above package repositories contains:

• CRAN: 11,795 packages, 5.8 GiB disk space
• BioCsoft: 1,476 packages, 4.2 GiB disk space
• BioCann: 910 packages, 61 GiB disk space
• BioCexp: 324 packages, 31 GiB disk space