Patch a few source code bugs (#188)

* explicitly cast sparse matrix * fix travis badge * bump patch version
zdk123 · Oct 20, 2021 · c463727 · c463727
1 parent ff528b2
commit c463727
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Showing 6 changed files with 13 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: SpiecEasi
 Title: Sparse Inverse Covariance for Ecological Statistical Inference
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: c(
     person("Zachary", "Kurtz", role = c("aut", "cre"), email="[email protected]"),
     person("Christian", "Mueller", role = "aut"),

diff --git a/README.Rmd b/README.Rmd
@@ -15,7 +15,7 @@ if (!runchunks) load('.README.RData')
 ```
 SpiecEasi
 =========
-[![Build Status](https://travis-ci.org/zdk123/SpiecEasi.svg?branch=pulsar)](https://travis-ci.org/zdk123/SpiecEasi)
+[![Build Status](https://app.travis-ci.com/zdk123/SpiecEasi.svg?branch=master)](https://app.travis-ci.com/zdk123/SpiecEasi)
 
 Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
 

diff --git a/README.md b/README.md
@@ -3,8 +3,7 @@
 SpiecEasi
 =========
 
-[![Build
-Status](https://travis-ci.org/zdk123/SpiecEasi.svg?branch=pulsar)](https://travis-ci.org/zdk123/SpiecEasi)
+[![Build Status](https://app.travis-ci.com/zdk123/SpiecEasi.svg?branch=master)](https://app.travis-ci.com/zdk123/SpiecEasi)
 
 Sparse InversE Covariance estimation for Ecological Association and
 Statistical Inference

diff --git a/src/ADMM.cpp b/src/ADMM.cpp
@@ -22,7 +22,7 @@ arma::mat sqrtmNewt2(arma::mat& C, arma::mat& sqrt0, const double& errTol) {
 
 arma::sp_mat SOFTTHRESH2(arma::mat& Sig, const float& lambda, const bool& shrinkDiag = true) {
     arma::mat A = symmatu(Sig);
-    int n = A.n_cols;
+//    int n = A.n_cols;
     arma::sp_mat S(sign(A));
     arma::mat    M(abs(A)-lambda);
     M.elem(find(M < 0)).zeros();
@@ -33,9 +33,9 @@ arma::sp_mat SOFTTHRESH2(arma::mat& Sig, const float& lambda, const bool& shrink
 
 
 void svdPowSym(arma::mat& U, arma::vec& d, arma::mat& V, arma::mat& A, int k, int q) {
-    int l = k;
+//    int l = k;
     int m = A.n_rows;
-    int n = A.n_cols;
+//    int n = A.n_cols;
     arma::mat P = randu<mat>(m,k-1);
     arma::mat Q, R;
     qr(Q, R, (P.t()*A).t());
@@ -190,7 +190,7 @@ List ADMM(const arma::mat& SigmaO, const double& lambda, arma::mat& I,
       }
 
       X.cols(0  , n-1  ) = R;
-      X.cols(n  , n*2-1) = S;
+      X.cols(n  , n*2-1) = arma::mat(S);
       X.cols(n*2, n*3-1) = L;
 
       RO = over_relax_par*R + (1-over_relax_par)*RY;

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -6,6 +6,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // ADMM
 List ADMM(const arma::mat& SigmaO, const double& lambda, arma::mat& I, arma::mat& Lambda, arma::mat& Y, double beta, int r, double mu, const double& eta, const double& muf, const int& maxiter, const double& newtol, const double& tol, const double& over_relax_par, bool shrinkDiag);
 RcppExport SEXP _SpiecEasi_ADMM(SEXP SigmaOSEXP, SEXP lambdaSEXP, SEXP ISEXP, SEXP LambdaSEXP, SEXP YSEXP, SEXP betaSEXP, SEXP rSEXP, SEXP muSEXP, SEXP etaSEXP, SEXP mufSEXP, SEXP maxiterSEXP, SEXP newtolSEXP, SEXP tolSEXP, SEXP over_relax_parSEXP, SEXP shrinkDiagSEXP) {

diff --git a/src/svthresh.cpp b/src/svthresh.cpp
@@ -8,7 +8,7 @@ using namespace arma;
 //soft thresholding operator of symmetric matrix
 arma::sp_mat SOFTTHRESH(arma::mat Sig, float lambda, bool shrinkDiag = true) {
     arma::mat A = symmatu(Sig);
-    int n = A.n_cols;
+//    int n = A.n_cols;
     arma::sp_mat S(sign(A));
     arma::mat    M(abs(A)-lambda);
     M.elem(find(M < 0)).zeros();