Hi, Team.
I am working on a package that uses RcppEigen. The package can be installed
successfully locally and passed CRAN auto-check. However, it cannot pass
the gcc-UBSAN test with the following error message: a problem with the LLT
function in Eigen. I am not sure how to fix this. Any suggestion or help is
highly appreciated!
rkriging.Rcheck/rkriging-Ex.Rout:/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Cholesky/LLT.h:66:49:
runtime error: load of value 20880, which is not a valid value for type
'ComputationInfo'
#0 0x7f967645dfc6 in Eigen::LLT<Eigen::Matrix<double, -1, -1, 0,
-1, -1>, 1>::operator=(Eigen::LLT<Eigen::Matrix<double, -1, -1, 0, -1,
-1>, 1>&&)
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Cholesky/LLT.h:66
#1 0x7f967645dfc6 in Kriging::Kriging(Eigen::Matrix<double, -1, -1,
0, -1, -1> const&, Eigen::Matrix<double, -1, 1, 0, -1, 1> const&,
Kernel&, bool const&)
/data/gannet/ripley/R/packages/incoming/rkriging.Rcheck/00_pkg_src/rkriging/src/kriging.cpp:26
#2 0x7f96769cac53 in
UniversalKriging::UniversalKriging(Eigen::Matrix<double, -1, -1, 0, -1,
-1> const&, Eigen::Matrix<double, -1, 1, 0, -1, 1> const&, Kernel&, bool
const&, unsigned long const&,
Rcpp::Function_Impl<Rcpp::PreserveStorage>)
/data/gannet/ripley/R/packages/incoming/rkriging.Rcheck/00_pkg_src/rkriging/src/kriging.cpp:385
#3 0x7f9676929f68 in Rcpp::Constructor_6<UniversalKriging,
Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, 1,
0, -1, 1>, Kernel&, bool, unsigned long,
Rcpp::Function_Impl<Rcpp::PreserveStorage> >::get_new(SEXPREC**, int)
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:115
#4 0x7f96767c091f in
Rcpp::class_<UniversalKriging>::newInstance(SEXPREC**, int)
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:131
#5 0x7f967c9d56a8 in class__newInstance(SEXPREC*)
/tmp/Rtmp7QBClZ/R.INSTALL19fb7f3cfc39c8/Rcpp/src/module.cpp:143
Thank you!
Best,
Chaofan
---------- Forwarded message ---------
From: Uwe Ligges <lig...@statistik.tu-dortmund.de>
Date: Tue, Jul 16, 2024 at 2:19 AM
Subject: Re: CRAN Submission rkriging 1.0.1
To: Bill Huang <10billhuan...@gmail.com>
Please ask on the mailing list <r-package-devel@r-project.org>
Best,
Uwe Ligges
On 16.07.2024 08:32, Bill Huang wrote:
> Hi, Uwe.
>
> Thanks for the message! I am not sure how to resolve this issue. Is
> there anyone you know that might be able to help me on this?
>
> Thank you!
> Best,
> Chaofan
>
> On Mon, Jul 15, 2024 at 11:44 AM Uwe Ligges
> <lig...@statistik.tu-dortmund.de
> <mailto:lig...@statistik.tu-dortmund.de>> wrote:
>
> Thanks, we still see with gcc-UBSAN
>
>
>
rkriging.Rcheck/rkriging-Ex.Rout:/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Cholesky/LLT.h:66:49:
> runtime error: load of value 20880, which is not a valid value for
type
> 'ComputationInfo'
> #0 0x7f967645dfc6 in Eigen::LLT<Eigen::Matrix<double, -1, -1, 0,
> -1, -1>, 1>::operator=(Eigen::LLT<Eigen::Matrix<double, -1, -1, 0, -1,
> -1>, 1>&&)
>
/data/gannet/ripley/R/test-dev/RcppEigen/include/Eigen/src/Cholesky/LLT.h:66
> #1 0x7f967645dfc6 in Kriging::Kriging(Eigen::Matrix<double,
> -1, -1,
> 0, -1, -1> const&, Eigen::Matrix<double, -1, 1, 0, -1, 1> const&,
> Kernel&, bool const&)
>
/data/gannet/ripley/R/packages/incoming/rkriging.Rcheck/00_pkg_src/rkriging/src/kriging.cpp:26
> #2 0x7f96769cac53 in
> UniversalKriging::UniversalKriging(Eigen::Matrix<double, -1, -1, 0,
-1,
> -1> const&, Eigen::Matrix<double, -1, 1, 0, -1, 1> const&, Kernel&,
> bool
> const&, unsigned long const&,
> Rcpp::Function_Impl<Rcpp::PreserveStorage>)
>
/data/gannet/ripley/R/packages/incoming/rkriging.Rcheck/00_pkg_src/rkriging/src/kriging.cpp:385
> #3 0x7f9676929f68 in Rcpp::Constructor_6<UniversalKriging,
> Eigen::Matrix<double, -1, -1, 0, -1, -1>, Eigen::Matrix<double, -1, 1,
> 0, -1, 1>, Kernel&, bool, unsigned long,
> Rcpp::Function_Impl<Rcpp::PreserveStorage> >::get_new(SEXPREC**, int)
>
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/Module_generated_Constructor.h:115
> #4 0x7f96767c091f in
> Rcpp::class_<UniversalKriging>::newInstance(SEXPREC**, int)
> /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/module/class.h:131
> #5 0x7f967c9d56a8 in class__newInstance(SEXPREC*)
> /tmp/Rtmp7QBClZ/R.INSTALL19fb7f3cfc39c8/Rcpp/src/module.cpp:143
>
>
> Please fix and resubmit.
>
> Best,
> Uwe Ligges
>
>
>
> On 13.07.2024 23:47, CRAN Package Submission Form wrote:
> >
> > [This was generated from CRAN.R-project.org/submit.html
> <http://CRAN.R-project.org/submit.html>]
> >
> > The following package was uploaded to CRAN:
> > ===========================================
> >
> > Package Information:
> > Package: rkriging
> > Version: 1.0.1
> > Title: Kriging Modeling
> > Author(s): Chaofan Huang [aut, cre], V. Roshan Joseph [aut]
> > Maintainer: Chaofan Huang <10billhuan...@gmail.com
> <mailto:10billhuan...@gmail.com>>
> > Depends: R (>= 3.0.2)
> > Description: An 'Eigen'-based computationally efficient 'C++'
> > implementation for fitting various kriging models to data.
> > This research is supported by U.S. National Science
> > Foundation grant DMS-2310637.
> > License: GPL (>= 2)
> > Imports: Rcpp, nloptr (>= 1.2.0), methods, stats
> > LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0), BH (>= 1.75.0.0),
> nloptr (>=
> > 1.2.0)
> >
> >
> > The maintainer confirms that he or she
> > has read and agrees to the CRAN policies.
> >
> > Submitter's comment: This is the resubmission of the package
> `rkriging` to
> > fix the issue from the CRAN checks. Please see
> > https://cran.rstudio.com/web/checks/check_results_rkriging.html
> <https://cran.rstudio.com/web/checks/check_results_rkriging.html>
> > for the previous check.
> >
> > =================================================
> >
> > Original content of DESCRIPTION file:
> >
> > Package: rkriging
> > Type: Package
> > Title: Kriging Modeling
> > Version: 1.0.1
> > Authors@R: c(
> > person(given = "Chaofan",
> > family = "Huang",
> > role = c("aut", "cre"),
> > email = "10billhuan...@gmail.com
> <mailto:10billhuan...@gmail.com>"),
> > person(given = "V. Roshan",
> > family = "Joseph",
> > role = c("aut"),
> > email = "ros...@gatech.edu <mailto:ros...@gatech.edu>")
> > )
> > Description: An 'Eigen'-based computationally efficient 'C++'
> implementation for fitting various kriging models to data. This
> research is supported by U.S. National Science Foundation grant
> DMS-2310637.
> > License: GPL (>= 2)
> > Depends: R (>= 3.0.2)
> > Imports: Rcpp, nloptr (>= 1.2.0), methods, stats
> > LinkingTo: Rcpp, RcppEigen (>= 0.3.3.5.0), BH (>= 1.75.0.0),
> nloptr (>=
> > 1.2.0)
> > Encoding: UTF-8
> > RoxygenNote: 7.1.2
> > NeedsCompilation: yes
> > Packaged: 2024-07-13 21:36:19 UTC; billhuang
> > Author: Chaofan Huang [aut, cre],
> > V. Roshan Joseph [aut]
> > Maintainer: Chaofan Huang <10billhuan...@gmail.com
> <mailto:10billhuan...@gmail.com>>
> >
>
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