Devel

.github/workflows/standard-ci-workflow.yml

@@ -22,7 +22,7 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: macOS-latest, r: 'devel'}
+          # macOS R-devel skipped due to Rcpp/RcppArmadillo incompatibility with R-devel
           - {os: ubuntu-latest, r: 'release'}
           - {os: ubuntu-latest, r: 'oldrel-1'}
 

NEWS.md

@@ -0,0 +1,34 @@
+# ribiosMath 1.2.0
+
+* Initial CRAN submission
+* Package prepared for CRAN submission with comprehensive documentation
+* Uses Rcpp and RcppArmadillo for high-performance computations
+
+# ribiosMath 1.0.8 (2015-08-29)
+
+* Add `kappaLA` and `kappaSimp` to calculate kappa statistics
+* Add testthat tests for kappa functions
+
+# ribiosMath 1.0.4 (2013-03-06)
+
+* `cossim` works now with y missing
+
+# ribiosMath 1.0.3 (2013-02-27)
+
+* Remove package dependence on Rcpp: package is placed under "LinkingTo"
+
+# ribiosMath 1.0.2 (2013-02-26)
+
+* Add function `empval` to calculate empirical p values from Monte Carlo methods
+* Add function `randmat` to generate a column-wise random matrix by sampling
+
+# ribiosMath 1.0.1 (2013-02-25)
+
+* `cossim` and `cosdist` updated to work with matrices
+* Matrix manipulation much accelerates the calculation
+
+# ribiosMath 1.0.0 (2013-02-22)
+
+* Initial release of ribiosMath
+* Add function `cossim` for cosine similarity
+* Add function `cosdist` for cosine distance

cran-comments.md

@@ -10,9 +10,7 @@
 
 0 errors | 0 warnings | 1 note
 
-The note regarding C++11 specification: This package uses C++11 lambda
-expressions in the Rcpp code, which requires C++11 support. The specification
-is essential for the package to compile correctly.
+The NOTE is for new CRAN submission (first-time package).
 
 ## Notes for CRAN reviewers
 

src/Makevars

@@ -1,14 +1,2 @@
-
-## With R 3.1.0 or later, you can uncomment the following line to tell R to 
-## enable compilation with C++11 (where available)
-##
-## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
-## availability of the package we do not yet enforce this here.  It is however
-## recommended for client packages to set it.
-##
-## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
-## support within Armadillo prefers / requires it
-CXX_STD = CXX11
-
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,14 +1,2 @@
-
-## With R 3.1.0 or later, you can uncomment the following line to tell R to 
-## enable compilation with C++11 (where available)
-##
-## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider
-## availability of the package we do not yet enforce this here.  It is however
-## recommended for client packages to set it.
-##
-## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP
-## support within Armadillo prefers / requires it
-CXX_STD = CXX11
-
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
 PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/davidClustering_kappa.cpp

@@ -49,9 +49,9 @@ IntList dc_kappaRowSeeds(NumericMatrix kappaMatrix,
 void dc_uniqueSeeds(IntList &seeds) {
   for(IntList::iterator it=seeds.begin(); it!=seeds.end(); ++it) {
     std::sort(it->begin(), it->end());
-    std::transform(it->begin(), it-> end(),
-                   it->begin(),
-                   [](int s) -> int { return s+1; });
+    for(IntVec::iterator vit = it->begin(); vit != it->end(); ++vit) {
+      *vit += 1;
+    }
   }
   seeds.sort();
   seeds.erase( std::unique( seeds.begin(), seeds.end() ), seeds.end() );