NEWS (original) (raw)

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 whenput-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 typeexpression, 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 besuppressedMessages-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 putparameters 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 inattach
fixed regression in dependencies (wrong plot edges)
fixed bug in set, was not working when settingsrc 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 andchunk 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 prjparameter in put. project items store session information automatically when put is called. Theinfo command works differently on projectitems.
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 andreplace
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 tographics: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 URLparameter
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 ofstash("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 toget.
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.