NEWS

ndexr 1.21.1

**UPDATE: Using the RCX package for working with networks.** **Defunct Functions:**
*rcx_fromJSON:* 'RCX::readJSON()'
*rcx_toJSON:* 'RCX::toCX()'
*rcx_aspect_toJSON:* 'rcx_aspect_toJSON'
*rcx_new:* 'RCX::createRCX()'
*rcx_asNewNetwork:* 'RCX::createRCX()'
*rcx_updateMetaData:* 'RCX::updateMetaData()'
*print.RCX:* 'RCX::print.RCX()'
*rcx_toRCXgraph:* 'RCX::toIgraph()'
*rcxgraph_toRCX* 'RCX::fromIgraph()'

**UPDATE: Using the RCX package for working with networks.** **Deprecated Functions:**
*rcx_fromJSON:* 'RCX::readJSON()'
*rcx_toJSON:* 'RCX::toCX()'
*rcx_aspect_toJSON:* 'rcx_aspect_toJSON'
*rcx_new:* 'RCX::createRCX()'
*rcx_asNewNetwork:* 'RCX::createRCX()'
*rcx_updateMetaData:* 'RCX::updateMetaData()'
*print.RCX:* 'RCX::print.RCX()'
*rcx_toRCXgraph:* 'RCX::toIgraph()'
*rcxgraph_toRCX* 'RCX::fromIgraph()'

FIX: error in RCX => RCXgraph => RCX conversion
FIX: NDEx server update for return columns in network list, summary and metadata; metadata also not nested anymore
FIX: tests crashed because of missing network; updated used UUID to new version of the public one from ndextutorials
exclude ..Rcheck from git; added "ndexr" to user agent header
FIX: build error caused by 'metadata:properties' now being optional
UPDATE: minor bugfixes due to ndex server update. Added api for ndex server version 2.2

**Breaking changes of the class and function names!** **NGraph** was renamed to **RCXgraph** to avoid naming Disambiguities! **Deprecated Functions:**
*rcx_toRCXgraph*
*rcxgraph_fromRCX*
*rcxgraph_toRCX*
*rcx_fromRCXgraph* Therefore the new funtions are called:
*rcx_toRCXgraph*
*rcxgraph_fromRCX*
*rcxgraph_toRCX*
*rcx_fromRCXgraph*

Changed the naming of the functions: dots are replaced by underscores, so that the functions may not be confused with S3 methods. The naming convention itself doesn't change! E.g. the new name of the function "ndex.network.update.aspect" is now "ndex_network_update_aspect"
Moved packages httr, jsonlite, plyr and tidyr from "Depends" field to "Imports" (Import into NAMESPACE not necessary, because external package function names are always explicitly qualified)
Fixed a bug in ngraph_fromRCX, which prevented the resulting ngraph object from node attributes to be set correctly. This also lead the following warnings: "Warning in vattrs[[name]][index] <- value : number of items to replace is not a multiple of replacement length"
Changed functions from passing a quoted string (e.g. host = "ndexConf$connection$host") as default parameter to using the actual object (e.g. host = ndexConf$connection$host)
Made some minor changes to NDExConnection object; removed an undesired warning.
Implement a print method for the classes "NDExConnection" and "RCX" to provide the user with a useful summary of this complicated object
changed to the usage of message() rather than cat() for verbose outputs, where it wasn't already done
Specified a single 'Maintainer' representing the primary contact for maintenance issues related to this package.
Removed the .gitignore file from this directory
Changed installation instructions in the vignette to Bioconductor