On 6 November 2019 at 08:43, Marcin Jurek wrote: | Hello, I'm trying to submit my package to CRAN and received the following | error message: | | Error(s) in re-building vignettes: | --- re-building ‘GPvecchia_vignette.Rmd’ using rmarkdown | .../RcppArmadillo/include/armadillo_bits/subview_meat.hpp:1223:54: | runtime error: reference binding to null pointer of type 'const unsigned | int' | ...//RcppArmadillo/include/armadillo_bits/access.hpp:26:100: runtime | error: reference binding to null pointer of type 'unsigned int' | ================================================================= | ==40666==ERROR: AddressSanitizer: heap-buffer-overflow on address | 0x615000445e48 at pc 0x7faebceeaa54 bp 0x7ffd4d87a980 sp 0x7ffd4d87a970 | READ of size 8 at 0x615000445e48 thread T0 | #0 0x7faebceeaa53 in createUcpp(Rcpp::Vector<14, | Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, | arma::Mat<double>, arma::Col<double>) | /data/gannet/ripley/R/packages/incoming/GPvecchia.Rcheck/00_pkg_src/GPvecchia/src/U_NZentries.cpp:366 | #1 0x7faebce84b2d in _GPvecchia_createUcpp | /data/gannet/ripley/R/packages/incoming/GPvecchia.Rcheck/00_pkg_src/GPvecchia/src/RcppExports.cpp:118 | | I have very little clue what to do, above all because I don't know how to | reproduce the error. Here is what I tried: | 1. Using the r-devel-san container from rocker. When I'm building the | package using | > RD CMD build GPvecchia | it tells me: | | Error: package or namespace load failed for ‘GPvecchia’ in dyn.load(file, | DLLpath = DLLpath, ...): | unable to load shared object | '/tmp/RtmpRfO4Ad/Rinst96f4db205fe/00LOCK-GPvecchia/00new/GPvecchia/libs/GPvecchia.so': | | /tmp/RtmpRfO4Ad/Rinst96f4db205fe/00LOCK-GPvecchia/00new/GPvecchia/libs/GPvecchia.so: | undefined symbol: __asan_option_detect_stack_use_after_return
That is strange. | Here is the package Makevars (following the specification from | https://www.stats.ox.ac.uk/pub/bdr/memtests/README.txt): | ## optional | CXX_STD = CXX11 | | #PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) | PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) -lasan | PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -fsanitize=address,undefined | -fno-omit-frame-pointer -fno-sanitize=vptr | PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) | | MAIN_LDFLAGS=-fsanitize=address,undefined -pthread | | F77 = gfortran -fsanitize=address | FC = gfortran -fsanitize=address | FCFLAGS = -g -O2 -mtune=native | FFLAGS = -g -O2 -mtune=native Because the r-devel-san Rocker container is already instrumented for (A)SAN at the r-devel level, you do not have say it again in your src/Makevars. This could be the source of you error here. Then again, it could be something else. Generally, SAN/ASAN/UBSAN debugging can be tedious. I built the Rocker container to reproduce a bug report I had at the time. The containers can then slip behind in their config -- but there are alternative ones as has been pointed out here: rhub is one, and I believe Winston et al also have one in the rstudio container stack. I used all of them, but at time still failed to reproduce errors at CRAN. In a world with more resources, someone somewhere could help CRAN to publish their containers. Then we would have reproducibility. Until then it is at times more like poking with a stick ... Dirk | 2. I also tried using r-hub and their platform with R compiled with the | appropriate flags. However, their configuration does not support openMP. | | Please help, thanks! | | Marcin | | [[alternative HTML version deleted]] | | ______________________________________________ | R-package-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-package-devel -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
