[R-pkg-devel] Mega2R CRAN submission: false positive

[Weeks, Daniel E]

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



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