Hello so I keep getting my package turned back because of errors detected
by UBSAN. I am trying to catch it using r-hub's platform with UBSAN but
there are no errors thrown there. What would be a good way for me to debug
this.
Obviously I did R CMD check --as-cran on my own machine, and on Travis and
I can't detect a thing.
What surprises me is that this is a runtime error and I wonder why all the
systems I test it on give it a pass...
Thanks for suggestions!
Marcin
-- Forwarded message -
From: Uwe Ligges
Date: Sat, Apr 18, 2020 at 2:32 AM
Subject: Re: CRAN submission GPvecchia 0.1.3
To: Marcin Jurek , CRAN <
cran-submissi...@r-project.org>
Thanks, we see:
checking with clang-UBSAN still has
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1277:23:
runtime error: reference binding to null pointer of type 'const unsigned
int'
#0 0x7f8b9133b5ae in arma::subview::colptr(unsigned
int)
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1277:12
#1 0x7f8b9133b5ae in arma::subview_col::subview_col(arma::Mat const&, unsigned int, unsigned
int, unsigned int)
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:3133:25
#2 0x7f8b913218d3 in arma::Col::head(unsigned int)
/data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/Col_meat.hpp:782:10
#3 0x7f8b913218d3 in clusterEqual(arma::Mat, int, int)
/data/gannet/ripley/R/packages/incoming/GPvecchia.Rcheck/00_pkg_src/GPvecchia/src/fastTree.cpp:53:35
#4 0x7f8b9132722d in knotTree(arma::Mat,
std::__1::map,
std::__1::allocator >, arma::Col,
std::__1::less,
std::__1::allocator > >,
std::__1::allocator, std::__1::allocator > const,
arma::Col > > >)
/data/gannet/ripley/R/packages/incoming/GPvecchia.Rcheck/00_pkg_src/GPvecchia/src/fastTree.cpp:241:21
#5 0x7f8b91328fae in generateNNarray(arma::Mat,
arma::Col, int, arma::Col, int)
/data/gannet/ripley/R/packages/incoming/GPvecchia.Rcheck/00_pkg_src/GPvecchia/src/fastTree.cpp:279:39
#6 0x7f8b91267769 in _GPvecchia_generateNNarray
/data/gannet/ripley/R/packages/incoming/GPvecchia.Rcheck/00_pkg_src/GPvecchia/src/RcppExports.cpp:93:34
and others not from this package.
Please fix the issue reported above and resubmit.
Best,
Uwe Ligges
On 16.04.2020 00:37, CRAN submission wrote:
> [This was generated from CRAN.R-project.org/submit.html]
>
> The following package was uploaded to CRAN:
> ===
>
> Package Information:
> Package: GPvecchia
> Version: 0.1.3
> Title: Scalable Gaussian-Process Approximations
> Author(s): Matthias Katzfuss [aut], Marcin Jurek [aut, cre], Daniel Zilber
>[aut], Wenlong Gong [aut], Joe Guinness [ctb], Jingjie Zhang
>[ctb], Florian Schaefer [ctb]
> Maintainer: Marcin Jurek
> Suggests: mvtnorm, knitr, rmarkdown, testthat
> Description: Fast scalable Gaussian process approximations, particularly
>well suited to spatial (aerial, remote-sensed) and
>environmental data, described in more detail in Katzfuss and
>Guinness (2017) . Package also contains a
>fast implementation of the incomplete Cholesky decomposition
>(IC0), based on Schaefer et al. (2019) and
>MaxMin ordering proposed in Guinness (2018)
>.
> License: GPL (>=2)
> Imports: Rcpp (>= 0.12.16), methods, stats, sparseinv, fields,
>Matrix(>= 1.2.14), parallel, GpGp, FNN
> LinkingTo: Rcpp, RcppArmadillo, BH
>
>
> The maintainer confirms that he or she
> has read and agrees to the CRAN policies.
>
> Submitter's comment: ### Resubmission 5
> This is a fifth resubmission
>
> *
>fixed problems reported in
>https://cran.r-project.org/web/checks/check_results_GPvecchia.html
>
>
>
>
>
> ###
>Resubmission 4
> This is a fourth resubmission
>
> * fixed
>a problem with unmatched variable types encountered
>during the last submission:
>runtime error:
>reference binding to null pointer of type 'const
>unsigned
>
> other check results as in submission
>3
>
>
>
>
>
>
> ### Resubmission 3
> This is a third
>resubmission
>
> * fixed the problem with variable types
>(unsigned int) in src/U_NZentries.cpp
>
>
> ## Test
>environments
> * local ubuntu 18.04, R 3.4.4
> * ubuntu
>16.04 (Travis CI), R-devel
> * Windows Server 2008 R2
>SP1, R-devel, 32/64 bit (R-hub)
>
> There was 1 NOTE:
> *
>checking installed package size ... NOTE
>installed
>size is 7.0Mb
>sub-directories of 1Mb or more:
>
>libs 6.5Mb
>
> This is not unexpected in packages with
>compiled code as observed by Dirk
>Eddelbuettel
>
https://stackoverflow.com/questions/53819970/r-package-libs-directory-too-large-after-compilation-to-submit-on-cran
>
>
>
>
>
>
> ###
>Resubmission 2
> This is a second resubmission.
>
> *
>fixed an alloc-dealloc-mismatch error as reported
>here
>
>https://cran.r-project.org/web/checks/check_results_GPvecchia.html
>
>
> ##
>
