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
