[Rcpp-devel] Fwd: CRAN submission growfunctions 0.12

Dirk Eddelbuettel edd at debian.org
Tue Dec 9 00:52:04 CET 2014


On 8 December 2014 at 18:38, terrance savitsky wrote:
| Hello Rcpp Developers,  I had earlier forwarded a report that initialization of
| arma::SpMat objects through as<arma::spmat>() in my package generated a memory
| management fault in valgrind for my package, growfunctions.   The issue was
| sourced (not by me) and a fix was incoporated at RcppArmadillo version 0.4.400
| (and I am now using 0.4.550.1.0 in this latest build).  I will remove use of
| the SpMat type from my package as it is not extensively employed, but perhaps
| the issue warrants further investigation for RcppArmadillo.  

One day we may come across someone who uses sparse matrices and also has both
the skill and motivation to investigate this.

As I don't use them, I am not likely to find or make the time for it.  

Thanks for he report,  Dirk




|  
| Thank you,  Terrance Savitsky 
| ---------- Forwarded message ----------
| From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
| Date: Mon, Dec 8, 2014 at 5:33 PM
| Subject: Re: CRAN submission growfunctions 0.12
| To: Terrance Savitsky <tds151 at gmail.com>, CRAN <cran at r-project.org>
| 
| 
| On 08/12/2014 22:04, Prof Brian Ripley wrote:
| 
| 
| 
| And valgrind is still reporting issues in Armadillo, e.g.
| 
| ==30106== Conditional jump or move depends on uninitialised value(s)==30106== 
|   at 0x15EE8D9A: operator!= (test-3.2/RcppArmadillo/include/armadillo_bits/
| SpMat_iterators_meat.hpp:239)
| ==30106==    by 0x15EE8D9A: arma::enable_if2<(arma::is_arma_type<arma::Gen
| <arma::Mat<double>, arma::gen_ones_diag> >::value&&arma::is_arma_sparse_type
| <arma::SpM
| at<double> >::value)&&arma::is_same_type<arma::Gen<arma::Mat<double>,
| arma::gen_ones_diag>::elem_type, arma::SpMat<double>::elem_type>::value,
| arma::Mat<arma::Gen<arma::Mat<double>, arma::gen_ones_diag>::elem_type>
| >::result arma::operator-
| <arma::Gen<arma::Mat<double>, arma::gen_ones_diag>, arma::SpMat<double> >
| (arma::Gen<arma::Mat<double>, arma::gen_ones_diag> const&, arma::SpMat<double>
| const&)
| (test-3.2/RcppArmadillo/include/armadillo_bits/operator_minus.hpp:281)
| ==30106==    by 0x15EE0FB1: IGMRFDPMIX (packages/incoming/growfunctions.Rcheck/
| 00_pkg_src/growfunctions/src/dpmix.cpp:66)
| ==30106==    by 0x480C3C: R_doDotCall (svn/R-devel/src/main/dotcode.c:655)
| ==30106==    by 0x48158F: do_dotcall (svn/R-devel/src/main/dotcode.c:1251)
| 
| /main/eval.c:2034)==30106==  Uninitialised value was created by a heap
| allocation
| ==30106==    at 0x4A09190: memalign (/data/gannet/ripley/Sources/srcF20/
| valgrind-3.10.1/coregrind/m_replacemalloc/vg_replace_malloc.c:760)
| ==30106==    by 0x4A092A7: posix_memalign (/data/gannet/ripley/Sources/srcF20/
| valgrind-3.10.1/coregrind/m_replacemalloc/vg_replace_malloc.c:913)
| ==30106==    by 0x15EECC85: acquire<unsigned int> (test-3.2/RcppArmadillo/
| includ
| e/armadillo_bits/memory.hpp:75)
| ==30106==    by 0x15EECC85: acquire_chunked<unsigned int> (test-3.2/
| RcppArmadill
| o/include/armadillo_bits/memory.hpp:111)
| ==30106==    by 0x15EECC85: Rcpp::traits::Exporter<arma::SpMat<double> >::get()
| (test-3.2/RcppArmadillo/include/RcppArmadilloAs.h:101)
| ==30106==    by 0x15EE1096: as<arma::SpMat<double> > (test-3.2/Rcpp/include/
| Rcpp
| /as.h:81)
| ==30106==    by 0x15EE1096: as<arma::SpMat<double> > (test-3.2/Rcpp/include/
| Rcpp/as.h:144)
| ==30106==    by 0x15EE1096: IGMRFDPMIX (packages/incoming/growfunctions.Rcheck/
| 00_pkg_src/growfunctions/src/dpmix.cpp:63)
| ==30106==    by 0x480C3C: R_doDotCall (svn/R-devel/src/main/dotcode.c:655)
| ==30106==    by 0x48158F: do_dotcall (svn/R-devel/src/main/dotcode.c:1251)
| 
| 
| 
| --
| Brian D. Ripley,                  ripley at stats.ox.ac.uk
| Emeritus Professor of Applied Statistics, University of Oxford
| 1 South Parks Road, Oxford OX1 3TG, UK
| 
| 
| 
| --
| Thank you, Terrance Savitsky
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http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org


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