[Genabel-commits] r909 - pkg/ProbABEL/src

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

Author: lckarssen
Date: 2012-05-21 21:29:21 +0200 (Mon, 21 May 2012)
New Revision: 909

Modified:
   pkg/ProbABEL/src/Makefile.am
   pkg/ProbABEL/src/main.cpp
Log:
In ProbABEL:
- src/main.cpp: Added flush commands when printing out the status messages. This may slow down I/O to the screen slightly, but in general that is nothing compared to load and run times. However, it actually makes the status messages usefull since now we know that (in case of a problem) the program actually stopped at the last message. 

- In src/Makefile.am: Added additional options (-Wall -O3) to the compile lines for the binaries. Almost all warnings have now been fixed. The remaining ones are fixed in Maarten's ProbABEL refactoring branch. The -O3 option was also enabled by default in the ProbABEL versions before the autotools integration.



Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am	2012-05-17 19:35:22 UTC (rev 908)
+++ pkg/ProbABEL/src/Makefile.am	2012-05-21 19:29:21 UTC (rev 909)
@@ -24,6 +24,8 @@
  include/R_ext/Print.h include/R_ext/Random.h include/R_ext/Utils.h	\
  include/R_ext/RS.h
 
+AM_CXXFLAGS = -Wall -O3
+
 bin_PROGRAMS = palinear palogist
 if BUILD_pacoxph
 ## Extra files for pacoxph
@@ -34,15 +36,15 @@
 endif
 
 palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palinear_CXXFLAGS = -DLINEAR
+palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS)
 
 palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
-palogist_CXXFLAGS = -DLOGISTIC
+palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS)
 
 pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS)	\
  $(RHEADERS) survS.h survproto.h
-pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include
-pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include
+pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
+pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
 
 ## Install these scripts in the bin directory as well:
 dist_bin_SCRIPTS = probabel.pl extIDS.pl

Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp	2012-05-17 19:35:22 UTC (rev 908)
+++ pkg/ProbABEL/src/main.cpp	2012-05-21 19:29:21 UTC (rev 909)
@@ -329,25 +329,20 @@
 	std::cout<<"you are running mmscore...\n";
     }
 
-    std::cout << "Reading data ...";
+    std::cout << "Reading data ..." << flush;
 
-
-
     if(inverse_filename != NULL)
     {
 	InvSigma inv(inverse_filename, &phd);
 	invvarmatrix = inv.get_matrix();
 	double par=1.; //var(phd.Y)*phd.nids/(phd.nids-phd.ncov-1);
 	invvarmatrix = invvarmatrix*par;
-	std::cout << " loaded InvSigma ...";
+	std::cout << " loaded InvSigma ..." << flush;
 	//	matrix.print();
     }
 
 
 
-
-    std::cout.flush();
-
     gendata gtd;
     if (!isFVF)
 	gtd.re_gendata(genfilename, nsnps, ngpreds, phd.nids_all, phd.nids,
@@ -356,7 +351,7 @@
 	gtd.re_gendata(str_genfilename, nsnps, ngpreds, phd.nids_all, phd.nids,
 		       phd.allmeasured, phd.idnames);
 
-    std::cout << " loaded genotypic data ...";
+    std::cout << " loaded genotypic data ..." << flush;
 
     /**
        if (isFVF)
@@ -372,7 +367,7 @@
     regdata nrgd(phd,gtd,-1);
 #endif
 
-    std::cout << " loaded null data ...";
+    std::cout << " loaded null data ..." << flush;
 
 #if LOGISTIC
     logistic_reg nrd(nrgd);
@@ -386,7 +381,7 @@
 #endif
     null_loglik = nrd.loglik;
 
-    std::cout << " estimated null model ...";
+    std::cout << " estimated null model ..." << flush;
 
     // end null
 #if COXPH
@@ -397,11 +392,9 @@
 
     std::cout << " formed regression object ...";
 
-    std::cout << " done\n";
-    std::cout.flush();
+    std::cout << " done\n" << flush;
 
 
-
     //________________________________________________________________
     //Maksim, 9 Jan, 2009