Release valr 0.8.3

[jayhesselberth]

Todo:

• remove rtracklayer dependency and use lifecycle::deprecate_stop() for read_bigwig() and read_gtf() (external library throwing gcc-ASAN errors #422 )
• Merge Use cpp11bigwig for read_bigwig() #425

Prepare for release:

• git pull
• Check current CRAN check results
• Polish NEWS
• usethis::use_github_links()
• urlchecker::url_check()
• devtools::build_readme()
• devtools::check(remote = TRUE, manual = TRUE)
• devtools::check_win_devel()
• revdepcheck::revdep_check(num_workers = 4)
• Update cran-comments.md
• git push

Submit to CRAN:

• usethis::use_version('patch')
• devtools::submit_cran()
• Approve email

Wait for CRAN...

• Accepted 🎉
• usethis::use_github_release()
• usethis::use_dev_version(push = TRUE)

[kriemo]

Thanks for starting this release. I’ll submit to CRAN after the holidays (the submissions are closed from dec. 23 – jan 7th).

[jayhesselberth]

I have a replacement for read_bigwig(). I will deposit on CRAN but the timing may not line up with including in the next release.

https://github.com/rnabioco/cpp11bigwig

[jayhesselberth]

cpp11bigwig was accepted by CRAN and should be online today. I can update to add as a dependency, and then we can proceed with this submission.

[jayhesselberth]

I restarted the checklist, better safe than sorry.

[kriemo]

There is a ASAN warning during package pre-testing on CRAN which they are requiring us to fix. Again It doesn't look like anything in our code but with a dependency.

File: valr-Ex.Rout
cleancall.c:110:46: runtime error: call to function cb_progress_done through pointer to incorrect function type 'void (*)(void *)'

File: tests/testthat.Rout
cleancall.c:110:46: runtime error: call to function cb_progress_done through pointer to incorrect function type 'void (*)(void *)'

This code is used in cli, ps,purrr. and processx.

https://win-builder.r-project.org/incoming_pretest/valr_0.8.3_20250108_153335/specialChecks/clang-san/

[kriemo]

Would you have the bandwidth to ask about how to fix this issue on the R-devel mailing list?

[jayhesselberth]

Now I'm confused. cb_progress_done is in purrr (which calls cli_progress_done). But none of valr, ps, or processx import purrr. And furthermore cli_progress_done() is used correctly in purrr, AFAICT, though the cast from SEXP to void might be the issue?

https://github.com/tidyverse/purrr/blob/700ce1973aa2dac714b7fbbbc619ead0fe946b0d/src/map.c#L14-L18

https://github.com/tidyverse/purrr/blob/700ce1973aa2dac714b7fbbbc619ead0fe946b0d/src/map.c#L31

[kriemo]

I've asked CRAN if they can provided the valr-Ex.Rout and tests/testthat.Rout files to help debug this. This looks to be quite a few dependencies away from our code so perhaps they may be willing to accept without a fix.

[jayhesselberth]

I confirmed that clang-asan fails on current purrr with a similar error to what we're seeing. This is in purrr-Ex.Rout from this rhub check.

cleancall.c:110:46: runtime error: call to function cb_progress_done through pointer to incorrect function type 'void (*)(void *)'
/__w/purrr/purrr/check/purrr.Rcheck/00_pkg_src/purrr/src/map.c:15: note: cb_progress_done defined here
    #0 0x7fd287f0d48b in call_exits /__w/purrr/purrr/check/purrr.Rcheck/00_pkg_src/purrr/src/cleancall.c:110:46
    #1 0x7fd28ddf1131 in R_ExecWithCleanup /tmp/R-devel/src/main/context.c:913:5
    #2 0x7fd287f0cdf2 in r_with_cleanup_context /__w/purrr/purrr/check/purrr.Rcheck/00_pkg_src/purrr/src/cleancall.c:133:14

The simple patch proposed on the R-devel mailing list fixes that clang-asan error (clang asan run).

I submitted tidyverse/purrr#1159

[kriemo]

Thanks so much for sending in a PR to purrr. I've notified CRAN that we submitted a patch to address the warning in purrr and I requested that valr 0.8.3 be accepted.

[kriemo]

received a quick response back that 0.8.3 was accepted and on it's way to CRAN