@@ -81,6 +81,6 @@ LazyDataCompression: xz

 BugReports: https://github.com/kasperdanielhansen/bsseq/issues

 biocViews: DNAMethylation

 SystemRequirements: C++11

-LinkingTo: Rcpp, Rhdf5lib, beachmat

+LinkingTo: Rcpp, beachmat

 NeedsCompilation: yes

 RoxygenNote: 6.1.0

@@ -2,11 +2,6 @@

 #define BSSEQ_H

 #include "Rcpp.h"

-#include "beachmat/integer_matrix.h"

-#include "beachmat/numeric_matrix.h"

-

-// TODO: Remove if not using std::runtime_error()

-#include <stdexcept>

 // Functions to be called from R.

 extern "C" {

@@ -16,6 +11,4 @@ extern "C" {

     SEXP check_M_and_Cov(SEXP, SEXP);

 }

-#include "utils.h"

-

 #endif

deleted file mode 100644

@@ -1,3 +0,0 @@

-BEACHMAT_LIBS=`echo 'beachmat::pkgconfig("PKG_LIBS")'|\

-    "${R_HOME}/bin/R" --vanilla --slave`

-PKG_LIBS=$(BEACHMAT_LIBS)

deleted file mode 100644

@@ -1,3 +0,0 @@

-BEACHMAT_LIBS=$(shell echo 'beachmat::pkgconfig("PKG_LIBS")'|\

-                "${R_HOME}/bin/R" --vanilla --slave)

-PKG_LIBS=$(BEACHMAT_LIBS)

@@ -1,5 +1,10 @@

 #include "BSseq.h"

+#include "beachmat/integer_matrix.h"

+#include "beachmat/numeric_matrix.h"

+

+#include "utils.h"

+

 // NOTE: Returning Rcpp::CharacterVector rather than throwing an error because

 //       this function is used within a validity method.

@@ -1,4 +1,4 @@

-#include "BSseq.h"

+#include "utils.h"

 // Special function to check for NA'ness.

@@ -1,6 +1,9 @@

 #ifndef UTILS_H

 #define UTILS_H

+// TODO: Not sure this is needed.

+#include "Rcpp.h"

+

 // Overloaded functions to check for NA'ness.

 bool isNA(int x);