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 <lig...@statistik.tu-dortmund.de> Date: Sat, Apr 18, 2020 at 2:32 AM Subject: Re: CRAN submission GPvecchia 0.1.3 To: Marcin Jurek <marcinjurek1...@gmail.com>, 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<unsigned int>::colptr(unsigned int) /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1277:12 #1 0x7f8b9133b5ae in arma::subview_col<unsigned int>::subview_col(arma::Mat<unsigned int> 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<unsigned int>::head(unsigned int) /data/gannet/ripley/R/test-clang/RcppArmadillo/include/armadillo_bits/Col_meat.hpp:782:10 #3 0x7f8b913218d3 in clusterEqual(arma::Mat<double>, 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<double>, std::__1::map<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, arma::Col<unsigned int>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, arma::Col<unsigned int> > > >) /data/gannet/ripley/R/packages/incoming/GPvecchia.Rcheck/00_pkg_src/GPvecchia/src/fastTree.cpp:241:21 #5 0x7f8b91328fae in generateNNarray(arma::Mat<double>, arma::Col<unsigned int>, int, arma::Col<unsigned int>, 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 <marcinjurek1...@gmail.com> > 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) <arXiv:1708.06302>. Package also contains a > fast implementation of the incomplete Cholesky decomposition > (IC0), based on Schaefer et al. (2019) <arXiv:1706.02205> and > MaxMin ordering proposed in Guinness (2018) > <arXiv:1609.05372>. > 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 > > > ## > Test environments > * local ubuntu 18.04, R 3.4.4 > * > ubuntu 16.04 (Travis CI), R 3.6.1 > * local OS X > install, R 3.5.1 > > ## R CMD check results > There were > no ERRORs or WARNINGs under either Ubuntu > version > > There were 2 NOTEs on Travis: > > * checking > installed package size ... NOTE > installed size is > 5.1Mb > sub-directories of 1Mb or more: > > libs > 4.6Mb > > 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 > > * > checking for hidden files and directories ... NOTE > > Found the following hidden files and directories: > > .travis.yml > These were most likely included in > error. See section ‘Package > structure’ in the > ‘Writing R Extensions’ manual. > > The said file is > listed in .Rbuildignore and the note goes away in the > local check of the build tarball > > > There was 1 NOTE > on local ubuntu installation: > > * checking installed > package size ... NOTE > installed size is 6.3Mb > > sub-directories of 1Mb or more: > libs 5.9Mb > > See > explanation above > > > > There was 1 WARNING under local > OS X: > > * checking whether package ‘GPvecchia’ > can be installed (41.2s) > Found the following > significant warnings: > Warning: package > ‘GpGp’ was built under R version 3.5.2 > > Local R > version used for development is 3.5.1 > > > > ## > Downstream dependencies > none > > ================================================= > > Original content of DESCRIPTION file: > > Package: GPvecchia > Type: Package > Title: Scalable Gaussian-Process Approximations > Version: 0.1.3 > Date: 2020-04-15 > Authors@R: c( > person("Matthias", "Katzfuss", role=c("aut"), email=" katzf...@gmail.com"), > person("Marcin", "Jurek", role=c("aut", "cre"), email=" marcinjurek1...@gmail.com"), > person("Daniel", "Zilber", role="aut"), > person("Wenlong", "Gong", role="aut"), > person("Joe", "Guinness", role="ctb"), > person("Jingjie", "Zhang", role="ctb"), > person("Florian", "Schaefer", role="ctb")) > Maintainer: Marcin Jurek <marcinjurek1...@gmail.com> > Author: Matthias Katzfuss [aut], > Marcin Jurek [aut, cre], > Daniel Zilber [aut], > Wenlong Gong [aut], > Joe Guinness [ctb], > Jingjie Zhang [ctb], > Florian Schaefer [ctb] > 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) <arXiv:1708.06302>. Package also contains a fast implementation of the incomplete Cholesky decomposition (IC0), based on Schaefer et al. (2019) <arXiv:1706.02205> and MaxMin ordering proposed in Guinness (2018) <arXiv:1609.05372>. > License: GPL (>=2) > Imports: Rcpp (>= 0.12.16), methods, stats, sparseinv, fields, > Matrix(>= 1.2.14), parallel, GpGp, FNN > LinkingTo: Rcpp, RcppArmadillo, BH > RoxygenNote: 6.1.1 > Suggests: mvtnorm, knitr, rmarkdown, testthat > VignetteBuilder: knitr > NeedsCompilation: yes > Packaged: 2020-04-15 22:36:32 UTC; marcin > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel