NEWS

repo 2.1.7 (2026-08-04)

Fixed NEWS.md formatting to comply with CRAN standards.

repo 2.1.6

fixed dependency issues as requested by CRAN
fixed reference DOI in description

repo 2.1.5 (2020-02-08)

fixed minor documentation bug as asked by CRAN

Now repo_info shows full paths.
Updated Readme

repo 2.1.4 (2019-12-19)

Completely renewed 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

repo 2.1.3.1

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

repo 2.1.3 (2018-05-16)

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).

repo 2.1.2.2

Changed error and warning calls with call.=F

repo 2.1.2.1

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.

repo 2.1.2 (2017-11-27)

Fixed broken link to remote sample
Changed the outputs of repo_check, which can now be suppressedMessages-ed.

repo 2.1.1 (2017-09-14)

Major release submitted to CRAN.

repo 2.1.1.0

CRAN candidate release.

Fixed bug in repo_build
Deprecated stash: now that put parameters are mostly optional, it is not necessary anymore.

repo 2.1.0.9001

Correcting vignette for next release
fixed version numbering (there is no v2.2)

repo 2.1.0.9000

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.

repo 2.1.0

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

repo 2.0.5.13

Added forking

repo 2.0.5.12

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

repo 2.0.5.11

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

repo 2.0.5.10

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

repo 2.0.5.8

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

repo 2.0.5.7

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.

repo 2.0.5.6

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.

repo 2.0.2 (2016-05-03)

new attr function in
attach now accepts URL parameter
2.0.2 is now the latest stable on CRAN

repo 2.0.1.3

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.

repo 2.0.1.2

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

repo 2.0.1.1

Bug fixes in lazydo and parameter check

repo 2.0.1.0

passes devtools::check()
stash simplified (now stash(x) instead of stash("x"))
Fixed bug when replacing entries due to new scheme for naming files.

repo 2.0.0

Bug fixes in lazydo
Minor additions to docs

repo 1.9.5

Fixed warnings in cpanel
All check() now passed
Merged latest fix from the dev branch
The NEWS file now used for main news

repo 1.9.4

Further testing
vignette updated
News moved to NEWS file
Minor release

repo 1.9.3

New pull feature now working
added lazydo (run expression and cache results)
Sources auto-attach suspended (had problems)

repo 1.9.0

Initial Shiny interface

repo 1.8.0

Sources are now auto-attached
Added safe-remove of data
Added auto-attach of sources
Added notes field

repo 1.7.2

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

repo 1.7.1

Added Bulk-edit feature.

repo 1.7.0

Added "Maybe-you-were-looking-for" feature to get.
Fixed bug with managing new relative paths.

repo 1.6.0

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.

repo 1.5.0

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

repo 1.0.0

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.