[rkward-devel] New breaking R2HTML release

[Milan Bouchet-Valat]

Dear maintainers of R packages depending on R2HTML,

We (the RKWard team and I) recently took over the maintainership of the
R2HTML package in order to prevent it from being archived on CRAN. To
this goal, we had to make a few (limited) breaking changes, which might
require your packages to be slightly adapted once it is uploaded to
CRAN. It is likely, though, that no change will be required at all.

For the record, packages depending on or suggesting R2HTML are:
affycoretools, AffyExpress, affylmGUI, Agreement, ArrayExpressHTS,
ArrayTools, ascii, clusterSim, DMRforPairs, EpiContactTrace, FFD,
HTMLUtils, limmaGUI, maigesPack, PKtools, psytabs, pubmed.mineR,
questionr, R453Plus1Toolbox, RcmdrPlugin.EACSPIR, RcmdrPlugin.temis,
RenextGUI, rgrs, rHVDM, STAR, SwimR

The list of breaking changes and of replacement solutions is short:
- .HTML.file is no longer stored in the global environment:
  use HTMLSetFile() and HTMLGetFile() instead of modifying it directly.
- .HTMLenv is no longer stored in the global environment:
  it should never have been accessed directly in the first place.
- fix() is no longer replaced during HTMLStart()/HTMLStop() sessions.
- Remove obsolete handling of 'date' class from package survival.
- Remove obsolete support for old format of objects from the rpart
package.

I have run R CMD check on most of your packages with the new R2HTML
version, and I found no problems. But please have a look, at least to
check whether you find any occurrences of ".HTML.file", which is likely
the most used of the features above. The new version can be found at
https://github.com/nalimilan/R2HTML
and you can install it easily using the devtools package, by the command
devtools::install_github("R2HTML", "nalimilan")

Any more general testing of R2HTML's feature is also welcome, as we are
not familiar with R2HTML and something might have been broken by
mistake.

I will wait for about ten days, and if nobody reports a problem I will
proceed and upload the new 2.3 version to CRAN. If you experience any
issue, please contact me and I'll delay the release.


Regards