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Transition to beachmat version 2

Peter Hickey authored on 23/04/2019 01:03:45
Showing7 changed files

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@@ -81,6 +81,6 @@ LazyDataCompression: xz
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 BugReports: https://github.com/kasperdanielhansen/bsseq/issues
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 biocViews: DNAMethylation
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 SystemRequirements: C++11
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-LinkingTo: Rcpp, Rhdf5lib, beachmat
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+LinkingTo: Rcpp, beachmat
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 NeedsCompilation: yes
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 RoxygenNote: 6.1.0
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@@ -2,11 +2,6 @@
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 #define BSSEQ_H
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 #include "Rcpp.h"
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-#include "beachmat/integer_matrix.h"
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-#include "beachmat/numeric_matrix.h"
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-
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-// TODO: Remove if not using std::runtime_error()
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-#include <stdexcept>
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 // Functions to be called from R.
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 extern "C" {
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@@ -16,6 +11,4 @@ extern "C" {
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     SEXP check_M_and_Cov(SEXP, SEXP);
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 }
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-#include "utils.h"
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-
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 #endif
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deleted file mode 100644
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@@ -1,3 +0,0 @@
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-BEACHMAT_LIBS=`echo 'beachmat::pkgconfig("PKG_LIBS")'|\
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-    "${R_HOME}/bin/R" --vanilla --slave`
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-PKG_LIBS=$(BEACHMAT_LIBS)
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deleted file mode 100644
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@@ -1,3 +0,0 @@
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-BEACHMAT_LIBS=$(shell echo 'beachmat::pkgconfig("PKG_LIBS")'|\
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-                "${R_HOME}/bin/R" --vanilla --slave)
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-PKG_LIBS=$(BEACHMAT_LIBS)
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@@ -1,5 +1,10 @@
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 #include "BSseq.h"
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+#include "beachmat/integer_matrix.h"
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+#include "beachmat/numeric_matrix.h"
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+
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+#include "utils.h"
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+
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 // NOTE: Returning Rcpp::CharacterVector rather than throwing an error because
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 //       this function is used within a validity method.
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@@ -1,4 +1,4 @@
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-#include "BSseq.h"
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+#include "utils.h"
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 // Special function to check for NA'ness.
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@@ -1,6 +1,9 @@
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 #ifndef UTILS_H
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 #define UTILS_H
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+// TODO: Not sure this is needed.
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+#include "Rcpp.h"
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+
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 // Overloaded functions to check for NA'ness.
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 bool isNA(int x);