external library throwing gcc-ASAN errors

[kriemo]

gcc-ASAN log

There is a gcc-ASAN error coming from our dependency rtracklayer, which originates in the UCSC library code vendored within rtracklayer (https://github.com/lawremi/rtracklayer/blob/32cd3c296c7609c44cad40eb38ff5e51a7dc95fa/src/ucsc/common.c#L32).

I can work with the rtracklayer maintainers to try to get this fixed. Otherwise we will need to rework read_bigwig and read_gtf to avoid this dependency until the ASAN error is fixed upstream.

This likely impacts dozens of packages depending on rtracklayer and
CRAN wants this fixed for valr by 2025-01-13.

[kriemo]

Actually this may only throw an error for us on CRAN, as we are the only package on CRAN with compiled code.

rt_rev_deps <- tools::package_dependencies("rtracklayer", reverse = TRUE)$rtracklayer
db <- tools::CRAN_package_db()
cran_rev_deps <- db[db$Package %in% rt_rev_deps, ]
cran_rev_deps[, c("Package", "LinkingTo", "NeedsCompilation")]
#>                       Package       LinkingTo NeedsCompilation
#> 2844                 CNVScope            <NA>               no
#> 3499            crispRdesignR            <NA>               no
#> 6704                    GALLO            <NA>               no
#> 6905                 geneHapR            <NA>               no
#> 9517                   kibior            <NA>               no
#> 10175              locuszoomr            <NA>               no
#> 14017  PlasmaMutationDetector            <NA>               no
#> 14018 PlasmaMutationDetector2            <NA>               no
#> 20957                    valr Rcpp (>= 1.0.0)              yes

^{Created on 2024-12-16 with reprex v2.1.1}

[jayhesselberth]

The wig package is an alternative for WIG reading: https://cran.r-project.org/web/packages/wig/

That's not useful, doesn't do bigwig.

[kriemo]

I'll work on reproducing this error on a linux machine, which will be necessary to show that we have fixed the error. In the meantime I'm skeptical that we will be able to patch this upstream in the core ucsc or vendored rtracklayer library.

To meet the CRAN deadline we may need to remove bigwig reading, at least temporarily. We could then work on implementing minimal support for reading bigwig files, perhaps with a minimal version of https://github.com/rnabioco/RcppLibBigWig as a separate package?

[jayhesselberth]

Yeah, let's eliminate rtracklayer as a dependency. I guess we should leave read_bigwig() and read_gtf() in the package. Those functions could just throwlifecycle::dreprecate_stop() for now, until we have another solution.

I forgot about RcppLibBIgWig! SHouldn't be hard to whip that into shape for CRAN. WIll look at that over the break.

[kriemo]

Ok sounds good! From: Jay Hesselberth ***@***.***> Date: Thursday, December 19, 2024 at 7:45 AM To: rnabioco/valr ***@***.***> Cc: Kent Riemondy ***@***.***>, Author ***@***.***> Subject: Re: [rnabioco/valr] external library throwing gcc-ASAN errors (Issue #422) Yeah, let's eliminate rtracklayer as a dependency. I guess we should leave read_bigwig() and read_gtf() in the package. Those functions could just throwlifecycle::dreprecate_stop() for now, until we have another solution. I forgot about RcppLibBIgWig! SHouldn't be hard to whip that into shape for CRAN. WIll look at that over the break. — Reply to this email directly, view it on GitHub<#422 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADIQEVKYGZ4IE3OWXOQZGGL2GLLZLAVCNFSM6AAAAABTWKD5BSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNJUGM4TCMZVGM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[jayhesselberth]

Looks like rtracklayer was removed from CRAN, we see a new error in valr on CRAN and this is a 404: https://cloud.r-project.org/web/packages/rtracklayer/index.html