https://gcc.gnu.org/bugzilla/show_bug.cgi?id=120837 suggests it's a compiler bug; hopefully the issue will go away once the version of gcc used on these CRAN check machines is updated.
On Thu, Jul 24, 2025 at 8:10 AM Weeks, Daniel E <we...@pitt.edu> wrote: > > Last week I saw that someone requested help because expected e-mails from > CRAN regarding an R package submission were not received. I am afraid I may > be in the same boat regarding trying to get our R package Mega2R fixed so it > can be in CRAN again, as I received no response regarding my pointing out > that the automated rejection of Mega2R is a false positive due to a compiler > bug that is beyond my capability to fix. > > I submitted Mega2R on July 14, 2025, and received an automated message that > > package Mega2R_1.2.0.tar.gz does not pass the incoming checks automatically. > > I responded as below that it was a false postive but did not receive any > response after that. > > -------------- > > I believe this rejection is a false positive due to a subtle compiler error. > > In June, our Mega2R package was rejected due to a Warning that was generated > during the CRAN checks. The Warning (which we are stilll seeing) was: > > ``` > Flavor: r-devel-linux-x86_64-debian-special-gcc-san > Check: Post-processing issues found for gcc-san, Result: WARNING > File: build_vignettes.log > vendor/sqlite3/sqlite3.c:80239:14: runtime error: load of address > 0x7faa31b1fa40 with insufficient space for an object of type 'struct > MemPage *' > ``` > > As I explain below, I think this Warning is not due to any mistake in Mega2R > code itself, but rather due to a compiler bug that is rarely encountered only > under specific settings. As such, I hope you will approve releasing Mega2R > to CRAN based on the following due diligence investigations and findings: > > Note that the Warning is generated by sqlite3 code so I opened a thread about > it on the SQLite forum: > > https://sqlite.org/forum/forumpost/e1015d1714 > > The conclusion of one investigation into this concludes that > > "Because of the requirements to reproduce the issue, it looks like a compiler > issue not a bug in SQLite" > > Further checks of Mega2R > > The Warning seen on the gcc-san test machine is not > reproducible on the other similar test machines. The warning is not > reproducible on the other machines. > > Further investigations via rhub > > https://github.com/r-hub2/diplomatic-mole-Mega2R/actions > > None of the checks on these machines reproduced the Warning seen on the > gcc-san test machine: > > clang-asan: All CRAN checks passed. > > clang-ubsan: All CRAN checks passed. > > valgrind: All CRAN checks passed. > > m1-san (R-devel): The Warning seen on the CRAN gcc-san test machine was not > observed. However, there was an error involving `seqlevels<-` (which is also > observed using R Under development (unstable) (2025-07-11 r88405)). This is > because the development version of `GenomeInfoDb` no longer contains the > `seqlevels<-` function, which in the next release > will be moved into the Seqinfo package. At that time, this Roxygen command > > ``` > #' @importMethodsFrom GenomeInfoDb 'seqlevels<-' > ``` > > will need to be updated. For now, in the currently released versions of R > such as R version 4.5.1 (2025-06-13), this is correct code. > ------------------------ > > > > Thanks, > > -- Dan -- > > Daniel E. Weeks, Ph.D. > Professor of Human Genetics > Professor of Biostatistics and Health Data Science > Department of Human Genetics > School of Public Health > University of Pittsburgh > Public Health 3119 > 130 DeSoto Street > Pittsburgh, PA 15261 > USA > > (412) 624-5388 > FAX: (412) 624-3020 > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
