Re-enabled all tests;

Disabled OPENMP compilation in an attempt to fix the failures on "Fedora clang" and "Solaris". Note that these errors could not be reproduced using devtools::check_rhub().

NEWS.md

@@ -1,13 +1,13 @@
 ---
 title: "NEWS about the PCMBaseCpp R-package"
 author: "Venelin Mitov"
-date: "20 November, 2019"
+date: "21 November, 2019"
 output: html_document
 ---
 
 # PCMBaseCpp 0.1.7
 
-* Disabled tests causing failures on CRAN "Fedora clang" and "Solaris" systems - none of these failures could be reproduced using `devtools::check_rhub()`.
+* Disabled OPENMP compilation in an attempt to fix the failures on "Fedora clang" and "Solaris". Note that these errors could not be reproduced using devtools::check_rhub().
 * Generated project web-page: https://venelin.github.io/PCMBaseCpp .
 
 # PCMBaseCpp 0.1.6

cran-comments.md

@@ -1 +1,96 @@
-Disabled test causing the failure on "Fedora clang". The errors could not be reproduced using devtools::check_rhub().
+---
+title: "NEWS about the PCMBaseCpp R-package"
+author: "Venelin Mitov"
+date: "21 November, 2019"
+output: html_document
+---
+
+Disabled OPENMP compilation in an attempt to fix the failures on "Fedora clang" and "Solaris". Note that these errors could not be reproduced using devtools::check_rhub(). Following is the e-mail exchange with Prof. Brian Ripley:
+
+
+Am Do., 14. Nov. 2019 um 17:36 Uhr schrieb Venelin Mitov <vmitov@gmail.com>:
+
+Dear Prof. Ripley, 
+Thanks for your message and for running the installation in debug mode. I've tested the package using devtools::check_rhub() and I only get notes for fedora-clang (screenshot below). 
+
+
+From the trace you've sent me, the error with fedora-clang seems to occur at line 1853 of SPLITT.h, which reads
+this->ptr_ = std::current_exception(); 
+Is it possible that the standard C++ function std::current_excpetion() does call terminateon f edora-clang? I don't have any way to reproduce the issue or test fixes on this platform. As for the solaris, there seems to be an additional error in the computation, because the logged values are taking random signs, while they should always be non-negative. Again, I don't have means to reproduce this issue:
+  what(): QuadraticPoly.h:InitNode:: The matrix V for node 15 (branch length=13.9031) is nearly singular or not positive definite; near 0 or negative eigenvalue found: -113.107; V.slice(i)(ki,ki)
+
+
+Best regards, Dr. Venelin Mitov
+
+
+Am Do., 14. Nov. 2019 um 12:37 Uhr schrieb Prof Brian Ripley <ripley@stats.ox.ac.uk>:
+See https://cran.r-project.org/web/checks/check_results_PCMBaseCpp.html .
+
+This version consistently fails on fedora-clang and Solaris.  Note that 
+a C++ program calling 'terminate' is contrary to the CRAN policies.  And 
+that is what is happening too with clang: running under gdb shows
+
+Thread 1 "R" received signal SIGSEGV, Segmentation fault.
+0x00007ffff56752c8 in typeinfo for std::logic_error ()
+    from /lib64/libstdc++.so.6
+
+(gdb) bt
+#0  0x00007ffff56752c8 in typeinfo for std::logic_error ()
+    from /lib64/libstdc++.so.6
+#1  0x00007fffedd17492 in __cxa_decrement_exception_refcount ()
+    from /usr/local/lib64/libc++abi.so.1
+#2  0x00007fffedd6b24f in 
+std::exception_ptr::operator=(std::exception_ptr const&) () from 
+/usr/local/lib64/libc++.so.1
+#3  0x00007fffe8ccd80d in SPLITT::ThreadExceptionHandler::CaptureException (
+     this=0x1a2a78b8) at ./SPLITT.h:1853
+#4 
+SPLITT::ThreadExceptionHandler::Run<SPLITT::PostOrderTraversal<PCMBaseCpp::BM>::TraverseTreeSingleThreadLoopPrunes()::{lambda()#1}>(SPLITT::PostOrderTraversal<PCMBaseCpp::BM>::TraverseTreeSingleThreadLoopPrunes()::{lambda()#1}) 
+(
+     this=0x1a2a78b8, f=...) at ./SPLITT.h:1847
+#5  0x00007fffe8cccf5d in 
+SPLITT::PostOrderTraversal<PCMBaseCpp::BM>::TraverseTreeSingleThreadLoopPrunes 
+(this=0x1a2a77f0) at ./SPLITT.h:2031
+#6  0x00007fffe8cccafd in 
+SPLITT::PostOrderTraversal<PCMBaseCpp::BM>::TraverseTree 
+(this=0x1a2a77f0, mode=<optimized out>) at ./SPLITT.h:1884
+#7  0x00007fffe8ccc9ef in 
+SPLITT::TraversalTask<PCMBaseCpp::BM>::TraverseTree (
+     this=0x1a2a5930, par=..., mode=4294662200) at ./SPLITT.h:582
+#8  0x00007fffe8c47d67 in 
+PCMBaseCpp::TraversalTaskWrapper<PCMBaseCpp::BM>::TraverseTree 
+(this=0x7ffffffb5838, par=..., mode=0) at ./QuadraticPolyCommon.h:127
+#9  0x00007fffe8cce193 in 
+Rcpp::CppMethod2<PCMBaseCpp::TraversalTaskWrapper<PCMBaseCpp::BM>, 
+std::__1::basic_string<char, std::__1::char_traits<char>, 
+std::__1::allocator<char> >, std::__1::vector<double, 
+std::__1::allocator<double> > const&, unsigned int>::operator() 
+(this=0x9197280, object=<optimized out>,
+     args=<optimized out>)
+     at 
+/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/module/Module_generated_CppMethod.h:195
+#10 0x00007fffe8cc9309 in 
+Rcpp::class_<PCMBaseCpp::TraversalTaskWrapper<PCMBaseCpp::BM> 
+ >::invoke_notvoid (this=<optimized out>, method_xp=<optimized out>,
+     object=0x1079b8b8, args=0x7ffffffb5ab0, nargs=2)
+     at 
+/data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/module/class.h:234
+#11 0x00007fffe9bfcab5 in CppMethod__invoke_notvoid (args=<optimized out>)
+     at module.cpp:220
+#12 0x000000000049dd6b in do_External (call=0xb987510, op=0x889268,
+     args=0xf33cac8, env=0xf33cb00)
+     at /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:572
+
+Please correct ASAP and before Nov 28 to safely retain the package on CRAN.
+
+-- 
+Brian D. Ripley,                  ripley@stats.ox.ac.uk
+Emeritus Professor of Applied Statistics, University of Oxford
+
+
+-- 
+Venelin MITOV
+
+
+-- 
+Venelin MITOV

src/Makevars

@@ -28,8 +28,11 @@
 # shared libraries. Yet, for these options to have an effect, the compiler itself
 # should support OpenMP, i.e. it should include the appropriate OpenMP headers,
 # and the openmp shared library binaries in its distribution (see above comments).
-PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_USE_OPENMP
-PKG_LIBS=$(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+#PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -DARMA_DONT_USE_OPENMP
+#PKG_LIBS=$(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+
+PKG_CXXFLAGS=-DARMA_DONT_USE_OPENMP
+PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
 # The following will set the compiler standard to C++11.
 CXX_STD = CXX11

tests/testthat/test-SingularV.R

@@ -1,6 +1,6 @@
 library(PCMBaseCpp)
 
-if(FALSE) {
+if(PCMBaseCppIsADevRelease()) {
   library(testthat)
   library(PCMBase)