Hi, I contacted some of you yesterday because your packages are breaking in R-devel.
Specifically these packages MAY have this issue: AffyTiling bgx CALIB Cardinal flipflop Ringo rMAT seqbias I may have said something like this: "Probably due to changes in R headers in recent R-devel. Please use recent R-devel to find and fix the problem." That's not super helpful (plus, what are R headers?). This may be more helpful. Here is Brian Ripley describing several affected packages: "These now fail to install in R-devel as they include headers such as R.h from C++ code inside an extern "C" block. That has been failing in some pre-release compilers and we have switched to including C++ headers such as cmath (rather than math.h). Installation now fails with current versions of common C++ compilers such as g++ and clang++." See also this excerpt from the NEWS file (https://github.com/wch/r-source/blob/trunk/doc/NEWS.Rd#L439-L449): \item When \R{} headers such as \file{R.h} and \file{Rmath.h} are called from C++ code in packages they include the C++ versions of system headers such as \file{<cmath>} rather than the legacy headers such as \file{<math.h>}. (Headers \file{Rinternals.h} and \file{Rinterface.h} already did, and inclusion of system headers can still be circumvented by defining \code{NO_C_HEADERS}, including as from this version for those two headers.) The manual has long said that \R{} headers should \bold{not} be included within an \code{extern "C"} block, and almost all the packages affected by this change are doing so. Hope this is more helpful. Dan _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
