[Rcpp-devel] Fwd: CRAN submission growfunctions 0.12

[terrance savitsky]

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.

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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