[Genabel-commits] r1393 - pkg/ProbABEL/src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-11-18 21:59:21 +0100 (Mon, 18 Nov 2013)
New Revision: 1393

Modified:
   pkg/ProbABEL/src/coxph_data.cpp
   pkg/ProbABEL/src/gendata.cpp
   pkg/ProbABEL/src/main.cpp
   pkg/ProbABEL/src/regdata.cpp
Log:
After the 'experiment' in the previous commit, which solved a valgrind error in Jenkins this change replaces the variable length arrays in the rest of the ProbABEL code with a proper C++ construct.


Modified: pkg/ProbABEL/src/coxph_data.cpp
===================================================================
--- pkg/ProbABEL/src/coxph_data.cpp	2013-11-18 20:33:22 UTC (rev 1392)
+++ pkg/ProbABEL/src/coxph_data.cpp	2013-11-18 20:59:21 UTC (rev 1393)
@@ -114,10 +114,13 @@
     {
         for (int j = 0; j < ngpreds; j++)
         {
-            double snpdata[nids];
+            double *snpdata = new double[nids];
             gend.get_var(snpnum * ngpreds + j, snpdata);
             for (int i = 0; i < nids; i++)
+            {
                 X.put(snpdata[i], i, (ncov - ngpreds + j));
+            }
+            delete[] snpdata;
         }
     }
 
@@ -129,8 +132,8 @@
     }
 
     // sort by time
-    double tmptime[nids];
-    int passed_sorted[nids];
+    double *tmptime = new double[nids];
+    int *passed_sorted = new int[nids];
 
     for (int i = 0; i < nids; i++)
     {
@@ -177,6 +180,9 @@
     // weights.print();
     // stime.print();
     // sstat.print();
+
+    delete[] tmptime;
+    delete[] passed_sorted;
 }
 
 void coxph_data::update_snp(gendata &gend, const int snpnum)
@@ -197,7 +203,7 @@
 
     for (int j = 0; j < ngpreds; j++)
     {
-        double snpdata[nids];
+        double *snpdata = new double[nids];
         for (int i = 0; i < nids; i++)
         {
             masked_data[i] = 0;
@@ -211,6 +217,7 @@
             if (std::isnan(snpdata[i]))
                 masked_data[order[i]] = 1;
         }
+        delete[] snpdata;
     }
 }
 
@@ -344,7 +351,9 @@
     mematrix<double> u(X.nrow, 1);
     mematrix<double> imat(X.nrow, X.nrow);
 
-    double work[X.ncol * 2 + 2 * (X.nrow) * (X.nrow) + 3 * (X.nrow)];
+    double *work = new double[X.ncol * 2 +
+                              2 * (X.nrow) * (X.nrow) +
+                              3 * (X.nrow)];
     double loglik_int[2];
     int flag;
 
@@ -435,4 +444,6 @@
             loglik = loglik_int[1];
         }
     }
+
+    delete[] work;
 }

Modified: pkg/ProbABEL/src/gendata.cpp
===================================================================
--- pkg/ProbABEL/src/gendata.cpp	2013-11-18 20:33:22 UTC (rev 1392)
+++ pkg/ProbABEL/src/gendata.cpp	2013-11-18 20:59:21 UTC (rev 1393)
@@ -30,7 +30,7 @@
     }
     else if (DAG != NULL)       // Read from fv file
     {
-        double tmpdata[DAG->getNumObservations()];
+        double *tmpdata = new double[DAG->getNumObservations()];
         DAG->readVariableAs((unsigned long int) var, tmpdata);
 
         unsigned int j = 0;
@@ -67,6 +67,7 @@
                 data[j++] = val;
             }
         }
+        delete[] tmpdata;
     }
     else
     {

Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp	2013-11-18 20:33:22 UTC (rev 1392)
+++ pkg/ProbABEL/src/main.cpp	2013-11-18 20:59:21 UTC (rev 1393)
@@ -634,8 +634,8 @@
         rgd.update_snp(gtd, csnp);
         double freq = 0.;
         unsigned int gcount = 0;
-        double snpdata1[gtd.nids];
-        double snpdata2[gtd.nids];
+        double *snpdata1 = new double[gtd.nids];
+        double *snpdata2 = new double[gtd.nids];
 
         if (input_var.getNgpreds() == 2) // Two predictors (probs)
         {
@@ -992,6 +992,8 @@
         }
 
         update_progress_to_cmd_line(csnp, nsnps);
+        delete[] snpdata1;
+        delete[] snpdata2;
     } // END for loop over all SNPs
 
 

Modified: pkg/ProbABEL/src/regdata.cpp
===================================================================
--- pkg/ProbABEL/src/regdata.cpp	2013-11-18 20:33:22 UTC (rev 1392)
+++ pkg/ProbABEL/src/regdata.cpp	2013-11-18 20:59:21 UTC (rev 1393)
@@ -82,10 +82,13 @@
     if (snpnum > 0)
         for (int j = 0; j < ngpreds; j++)
         {
-            double snpdata[nids];
+            double *snpdata = new double[nids];
             gend.get_var(snpnum * ngpreds + j, snpdata);
             for (int i = 0; i < nids; i++)
+            {
                 X.put(snpdata[i], i, (ncov - ngpreds + 1 + j));
+            }
+            delete[] snpdata;
         }
         // for (int i=0;i<nids;i++)
         //     for (int j=0;j<ngpreds;j++)
@@ -100,7 +103,7 @@
 
     for (int j = 0; j < ngpreds; j++)
     {
-        double snpdata[nids];
+        double *snpdata = new double[nids];
         for (int i = 0; i < nids; i++)
         {
             masked_data[i] = 0;
@@ -116,6 +119,7 @@
                 masked_data[i] = 1;
             }
         }
+        delete[] snpdata;
     }
 }