News

Feb 5, 2020, v2.1.5

• fixed minor documentation bug as asked by CRAN

Dec 22, 2019, v2.1.4.1

• Now repo_info shows full paths.
• Updated Readme

Dec 18, 2019, v2.1.4

• Completely renewd naming convention for the stored files. This change is transparent to the user and will not affect previous code. Also existing repositories can be used with this new version (previous files will be left untouched, new ones will follow the new convention). But now the directory tree of the repository has been greatly simplified and is human readable. Each item is stored 1 level (as opposed to 3) under the repo root and using a sanitized version of the item name (as opposed to a random string). Possible name collisions are avoided by appending a progressive number. Item name is still stored as is in the repository (and will still collide with previously stored items by the same name as expected).

• fix in the vignette to pass CRAN checks on some platforms

Dec 3, 2018, v2.1.3.1

• repo_get now allows to suppress name suggestions for faster search in large repositories.

May 4, 2018, v2.1.3

• Significant speedup of all operations involving a search through the items, including find and print. These are now usable with large repositories (tested with tens of thousands items).

Dic 6, 2017, v2.1.2.2

• Changed error and warning calls with call.=F

Nov 27, 2017, v2.1.2.1

• stash is not deprecated anymore, as it is useful to lazydo

• fixed some stash behaviour, like when put-ing an item with the same name of stash-ed item, which now does not throw an error.

• lazydo with force=T will not throw an error for existing item, which is now a stash-ed item

• laxydo now does not take an object of type expression, but an expression directly.

11/18/17, v2.1.2

• Fixed broken link to remote sample

• Changed the outputs of repo_check, which can now be suppressedMessages-ed.

08/03/17, v2.1.1 - Major release submitted to CRAN

08/01/17, v2.1.1 - CRAN candidate release

• Fixed bug in repo_build

• Deprecated stash: now that put parameters are mostly optional, it is not necessary anymore.

07/25/17, v2.1.0.9001

• Correcting vignette for next release

• fixed version numbering (there is no v2.2)

04/15/17, v2.1.0.9000

• Also the item name in put is now optional. If not provided, the name of the obj variable will be used.

• The chunk format has been simplified, the close tag is now just }, as follows:

    ## chunk "ChunkName" {
        ## ...
    ## }

• Some documentation updates.

04/11/17, v2.1.0

New features:

• Descriptions and tags are no more mandatory
• Alternative versions of the same chunk can now be defined like this:

    ## chunk "ChunkName#fork1"{
        ## ...
    ## chunk "ChunkName#fork1"}
    ## chunk "ChunkName#fork2"{
        ## ...
    ## chunk "ChunkName#fork2"}
    ## the following sets the active chunk:
    rp$options(chunk="fork")

Outputs from different forks will be stored together in the repo but all operations will refer to the output of the active chunk. This is to be better documented.

Change log:

• descriptions and tags are no more mandatory also in attach
• fixed regression in dependencies (wrong plot edges)
• fixed bug in set, was not working when setting src parameter

03/05/17, v2.0.5.13

• Added forking

03/04/17, v2.0.5.12

• Added depends function
• Added load function
• Added force parameter to build
• More documentation updates

02/24/17, v2.0.5.11

• Runs all checks
• Documentation updated
• dependencies now accepts overriding of default visual igraph parameters

02/22/17

• A paper about Repo has been published in BMC Bioinformatics.
• Added some testing code.

10/18/16, v2.0.5.8

• Major code refactoring. Direct call of repo_* function now deprecated.

10/14/16

• added chunk and build functions and chunk parameter to put. Repo can now associate a specific chunk of code with a resources and rebuild it upon request.
• added support for special project items and corresponding project function and prj parameter in put. project items store session information automatically when put is called. The info command works differently on project items.
• Improved aesthetics for the dependency graph through default visual parameters.
• added testthat support for internal tests
• added options function to set put default parameters.

10/08/16

• added buildURL parameter to set. It will add an URL to all items, such that it can be used is the repository is uploaded to a website.

• get can now be used on attachments, returns file path

• Fixed bugs in attach not working with attachments

• Fixed a few bugs with copy when copying multiple items. Now also accepts confirm and replace

• Added related function to extract items directly or indirectly related to an input item.

• added internal testthat unit testing

• A few changes to pies and dependencies. They now support additional parameters (…) to pass to graphics:pie and igraph:plot respectively. pies now merges together all items with size < 5% of the total. dependencies now supports tags to filter nodes to be showed. Also missing documentation for pies has been added.

05/03/16

• new attr function in

• attach now accepts URL parameter

• 2.0.2 is now the latest stable on CRAN

05/02/16

• 2.0.2 contains a fix to repo$pull for OS X

• Documentation updated

• NOTE: previous change implies that not all items have a “source” field. This does not seem to be a problem. However, older items storing current working directory as source could be affected.

04/28/16

• now src must be an item (meant to be an attachment containing source code). Documentation updated accordingly.

• minor updates to vignette

04/27/2016

• Bug fixes in lazydo and parameter check

04/24/2016

• passes devtools::check()

• stash simplified (now stash(x) instead of stash("x"))

• Fixed bug when replacing entries due to new scheme for naming files.

01/04/2016

• Bug fixes in lazydo

• Minor additions to docs

03/20/3026

• Fixed warnings in cpanel

• All check() now passed

• Merged latest fix from the dev branch

• The NEWS file now used for main news

03/19/2016

• Further testing

• vignette updated

• News moved to NEWS file

• Minor release

03/18/2016

• New pull feature now working

• added lazydo (run expression and cache results)

• Sources auto-attach suspended (had problems)

12/07/2015

• Initial Shiny interface

11/19/2015

• Sources are now auto-attached

• Added safe-remove of data

• Added auto-attach of sources

• Added notes field

10/21/2015

• Fixed regression in check after moving to relative paths

• Added check points for reserved tags and warnings for existing tags

• Improved print reaction when all matching results are hidden

10/19/2015

• Added Bulk-edit feature.

10/17/2015

• Added “Maybe-you-were-looking-for” feature to get.

• Fixed bug with managing new relative paths.

10/12/2015

• Absolute to relative paths for stored objects. This allows to easily rebase a repository, for example to a remote machine, without affecting the index.

• Automatic update of old repository entries upon resource loading.

10/08/2015

• Atomization of item replacement to avoid the possibility of data loss.

Earlier…

• Added search field in print to match anything in items and the corresponding “find” shortcut method.

• When using multiple tags now by default they match when at least one matches (OR).

• Now tags can be matched using OR, AND, NOT or any external logical function.

• Fixed a bug in print when showing one item.