Dear Bioconductor package developers, The XML package on CRAN has been compiling with an increasing number of deprecation warnings. Most of these are solvable, so the package is not going away and will keep working. Unfortunately, the following functions depend on undocumented interfaces that libxml2 maintainers no longer wish to support:
parseDTD dtdElement dtdElementValidEntry dtdEntity dtdIsAttribute dtdValidElement xmlContainsElement xmlContainsEntity They comprise the "DTD introspection" API. (Not the DTD validation interface: that's still supported.) The DTD object also used to be returned in the second element of the list (named $dtd) by functions xmlTreeParse(getDTD=TRUE), xmlInternalTreeParse(getDTD=TRUE), xmlNativeTreeParse(getDTD=TRUE), htmlTreeParse(getDTD=TRUE), htmlParse(getDTD=TRUE). I won't change the shape of the overall return value (since most users rely on what's returned with getDTD=TRUE argument by default), but the dtd element is going to become an empty list. Chances are that no current CRAN or Bioconductor uses these interfaces. (I ran checks including all direct reverse dependencies. Flaky Internet resources aside, there were no changes to worse.) Since the compilation warnings really need to be solved very soon (any other CRAN package with this many problems would be archived by now), these functions will most likely be disabled in the next version of XML. They'll still exist, but they won't return anything useful. If you really need them to work, please let me know and we'll try to come up with a different solution. -- Best regards, Ivan _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
