Merge pull request #106 from kbroman/cran

Fix compiler warnings on CRAN

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, cran]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, cran]
 
 name: R-CMD-check
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qtl
-Version: 1.62
-Date: 2023-11-17
+Version: 1.66
+Date: 2023-11-27
 Title: Tools for Analyzing QTL Experiments
 Author: Karl W Broman <[email protected]> and Hao Wu, with
   ideas from Gary Churchill and Saunak Sen and contributions from

NEWS.md

@@ -1,5 +1,15 @@
 # Revision history for the R/qtl package
 
+## Version 1.66, 2023-11-27
+
+### Bug fixes
+
+- Fixed problem in a call to Rprintf() in C++ code, identified by CRAN.
+  (Issue #104.)
+
+- Fixed additional compiler warnings on CRAN (Issue #105).
+
+
 ## Version 1.62, 2023-11-17
 
 ### Bug fixes

inst/INSTALL_ME.txt

@@ -39,10 +39,10 @@ INSTALLATION OF R AND R/QTL (Windows)
 
      This will download the binary from CRAN and install it.
 
-     Alternatively, you can download the "qtl_1.62.zip" (or the
+     Alternatively, you can download the "qtl_1.66.zip" (or the
      equivalent).  Then start R and select (on the menu bar)
      "Packages" and then "Install package from local zip file...".
-     Find the file "qtl_1.62.zip" on your hard drive, and click
+     Find the file "qtl_1.66.zip" on your hard drive, and click
      "Open".
 
 
@@ -58,7 +58,7 @@ INSTALLATION OF R AND R/QTL (MacOS version 10.13 and above)
      This will download the binary from CRAN and install it.
 
      Alternatively, download the compiled version of R/qtl for
-     Mac OS X, a file like "qtl_1.62.tgz".  Then start R and
+     Mac OS X, a file like "qtl_1.66.tgz".  Then start R and
      select (on the menu bar) "Packages & Data" -> "Package
      Installer".  Select "Local Binary Package" from the drop-down
      menu at the top of the window that comes up.  Click "Install"
@@ -78,19 +78,19 @@ INSTALLATION OF R/QTL (Unix)
      This will download the binary from CRAN and install it.
 
      Alternatively, download the R/qtl source code (a file like
-     "qtl_1.62.tar.gz").  Go into the directory containing the
+     "qtl_1.66.tar.gz").  Go into the directory containing the
      file and do one of the following:
 
      a. To install R/qtl in the standard location
         (/usr/local/lib/R/library), type
 
-            R CMD INSTALL qtl_1.62.tar.gz
+            R CMD INSTALL qtl_1.66.tar.gz
 
         You'll probably need to be superuser.
 
      b. To install the package locally, type
 
-            R CMD INSTALL --library=/home/auser/Rlibs qtl_1.62.tar.gz
+            R CMD INSTALL --library=/home/auser/Rlibs qtl_1.66.tar.gz
 
         (where "/home/auser/Rlibs" should be replaced with the
         appropriate directory).

src/mqmaugment.cpp

@@ -2,7 +2,7 @@
  *
  * mqmaugment.cpp
  *
- * Copyright (c) 1996-2011 by
+ * Copyright (c) 1996-2023 by
  * Ritsert C Jansen, Danny Arends, Pjotr Prins and Karl W Broman
  *
  * initial MQM C code written between 1996-2002 by Ritsert C. Jansen
@@ -241,7 +241,7 @@ int mqmaugmentfull(MQMMarkerMatrix* markers,int* nind, int* augmentednind, ivect
       (*augmentednind)=(*augmentednind)+(numimputations*current_leftover_ind);
       (*nind)= (*nind)+(current_leftover_ind);
       debug_trace("nind:%d,naugmented:%d",(*nind)+(current_leftover_ind),(*augmentednind)+(current_leftover_ind));
-      Rprintf("INFO: VALGRIND MEMORY DEBUG BARRIERE TRIGGERED\n", "");
+      Rprintf("INFO: VALGRIND MEMORY DEBUG BARRIERE TRIGGERED\n");
     }else{
       if(ind_still_left && augment_strategy == 3){
         if(verbose) Rprintf("INFO: Dropping %d individuals from further analysis\n",ind_still_left);

src/mqmdatatypes.cpp

@@ -196,8 +196,11 @@ void copyvector(vector vsource, vector vdestination, int dim) {
 
 #ifndef ENABLE_C99_MACROS
   void fatal(const char* s, ...){
-    Rf_error(s);
+      Rprintf("%s", s);
+      Rf_error("Fatal error\n");
   }
   void debug_trace(const char*, ...){}
-  void info(const char* s, ...){ Rprintf("INFO: "); Rprintf(s); Rprintf("\n"); }
+  void info(const char* s, ...){
+      Rprintf("INFO: %s\n", s);
+  }
 #endif