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Repo

Repo is a data-centered data flow manager. It allows to store R data files in a central local repository, together with tags, annotations, provenance and dependence information. Any saved object can then be easily located and loaded through the repo interface.

A paper about Repo has been published in BMC Bioinformatics.

Latest news are found in the NEWS.md file of the "Untested" branch.

Repo is developed by Francesco Napolitano

Minimal example

Repository creation in the default folder:

    library(repo)
    rp <- repo_open()

Putting some stuff (it is saved on permanent storage). In this case, just values and names are specified:

    rp$put(Inf, "God")
    rp$put(0, "user")

Putting specifying dependencies:

    rp$put(pi, "The Pi costant", depends="God")
    rp$put(1:10, "r", depends="user")

Getting stuff from the repository on the fly:

    diam <- 2 * rp$get("r")
    circum <- 2 * rp$get("The Pi costant") * rp$get("r")
    area <- rp$get("The Pi costant") * rp$get("r") ^ 2

Putting with verbose descriptions:

    rp$put(diam, "diameters", "These are the diameters", depends = "r")
    rp$put(circum, "circumferences", "These are the circumferences",
           depends = c("The Pi costant", "r"))
    rp$put(area, "areas", "This are the areas",
           depends = c("The Pi costant", "r"))

Repository contents:

    print(rp)
#>              ID Dims Size
#>             God    1 42 B
#>            user    1 40 B
#>  The Pi costant    1 45 B
#>               r   10 60 B
#>       diameters   10 65 B
#>  circumferences   10 94 B
#>           areas   10 93 B

    rp$info()
#> Root:            /tmp/RtmpIjPq16/kZJJAjPdwgCB 
#> Number of items: 7 
#> Total size:      439 B

    rp$info("areas")
#> ID:           areas
#> Description:  This are the areas
#> Tags:         
#> Dimensions:   10
#> Timestamp:    2017-08-04 15:40:03
#> Size on disk: 93 B
#> Provenance:   
#> Attached to:  -
#> Stored in:    sk/nr/zy/sknrzyen718nms80t89timt6fyrc2zvx
#> MD5 checksum: 65b946a5ffd6d1a63572e1ccfe3a9e08
#> URL:          -

Visualizing dependencies:

    rp$dependencies()

Development branches

• Master: stable major releases, usually in sync with lastest CRAN version.

• Dev: fairly stable minor releases.

• Untested: unstable, in progress versions. Latest news appear in the "NEWS.md" file of this branch.

Manuals

Besides inline help, two documents are available as introductory material:

• A paper published on BMC Bioinformatics

• An introductory vignette.

Download and Installation

Repo is on CRAN and can be installed from within R as follows:

> install.packages("repo")

However, CRAN versions are not updated very often. Latest stable release can be downloaded from Github at https://github.com/franapoli/repo. Repo can then be installed from the downloaded sources as follows:

> install.packages("path-to-downloaded-source", repos=NULL)

devtools users can download and install at once the latest development version from github as follows:

> install_github("franapoli/repo", ref="dev")