Hi Ivan, This is extremely helpful! I appreciate your time and detailed explanation.
Tracy > On May 8, 2025, at 6:30 PM, Ivan Krylov <ikry...@disroot.org> wrote: > > В Thu, 8 May 2025 12:01:47 -0400 > Tracy Morrison Sweet <tsw...@umd.edu> пишет: > >> New submission >> Package was archived on CRAN >> >> I’m not sure how to do anything to remove this note. > > This note is to be expected. > >> In process.txt and summary.txt, it says "File: HLSM-Ex.Rout >> vendor/cigraph/src/constructors/adjacency.c:87:34: runtime error: nan >> is outside the range of representable values of type ‘long’" > > The link to the original issue that got your package archived is more > informative because it contains the backtrace and shows the place in > your examples where the problem happens: > > https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-UBSAN/HLSM/HLSM-Ex.Rout > >>> fixed.fit = HLSMfixedEF(Y = ps.advice.mat, senderCov=ps.node.df, >> + initialVals = initialVals,priors = priors, >> + tune = tune,tuneIn = FALSE,dd = 2,niter = niter) >> core/constructors/adjacency.c:47:26: runtime error: nan is outside >> the range of representable values of type 'long' #0 0x7f09504c6e4b in >> igraph_i_adjacency_directed >> /tmp/Rtmp9HF8V2/R.INSTALL659cd504fd46b/igraph/src/core/constructors/adjacency.c:47:26 >> #1 0x7f09504c5715 in igraph_adjacency >> /tmp/Rtmp9HF8V2/R.INSTALL659cd504fd46b/igraph/src/core/constructors/adjacency.c:212:9 >> #2 0x7f0950c654a3 in R_igraph_graph_adjacency >> /tmp/Rtmp9HF8V2/R.INSTALL659cd504fd46b/igraph/src/rinterface_extra.c:4861:3 > > The file path is now different, but the issue is most likely the same. > During a call to HLSMfixedEF(), a matrix containing a NaN value is > passed to the 'igraph' package, where the NaN is converted to an > integer: > > https://github.com/igraph/rigraph/blob/9a2816248eb837077b5af28bad7b1b9c0713b128/src/vendor/cigraph/src/constructors/adjacency.c#L87 > > Unfortunately, converting a NaN into an integer is undefined behaviour > according to the C standard. The program is allowed to do literally > anything, so it caused your package to be archived. > > Ideally, 'igraph' could produce an informative error message upon > detecting a NaN, but you can avoid the problem on your end by making > sure that all values in your adjacency matrices are finite before > calling igraph::graph.adjacency(). > > To see the problem for yourself, you'll need a "sanitized" build of R: > https://cran.r-project.org/doc/manuals/R-exts.html#Using-Undefined-Behaviour-Sanitizer > > Sanitizers are somewhat finicky to use. The container images > docker.io/rocker/r-devel-ubsan-clang and > ghcr.io/r-hub/containers/clang-ubsan, or the R-hub service may help. > > Good luck! If this wasn't detailed enough, don't hesitate to ask > follow-up questions. > > -- > Best regards, > Ivan Tracy M. Sweet Associate Professor HDQM University of Maryland tsw...@umd.edu she/her/hers UMD Land Acknowledgement <https://diversity.umd.edu/resources/land-acknowledgement> [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
