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rnabioco / valr

Genome Interval Arithmetic in R

Home Page:http://rnabioco.github.io/valr/

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Release valr 0.6.1

jayhesselberth opened this issue · comments

commented

Prepare for release:

  • #353
  • devtools::build_readme()
  • Check current CRAN check results
  • devtools::check(remote = TRUE, manual = TRUE)
  • devtools::check_win_devel()
  • rhub::check_for_cran()
  • rhub::check(platform = 'ubuntu-rchk')
  • rhub::check_with_sanitizers()
  • revdepcheck::revdep_check(num_workers = 4)
  • Update cran-comments.md
  • Polish NEWS
  • Draft blog post

Submit to CRAN:

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

Wait for CRAN...

  • Accepted 🎉
  • usethis::use_github_release()
  • usethis::use_dev_version()
  • Finish blog post
  • Tweet
  • Add link to blog post in pkgdown news menu
commented

@kriemo How did you get rhub::check(platform = 'ubuntu-rchk') to work? I keep getting an error that IRanges etc are not installed. Did you have to set _R_CHECK_FORCE_SUGGESTS_ = "false"?

commented

I didn't set anything special just ran rhub::check(platform = 'ubuntu-rchk') :

Here's the last build report:
https://builder.r-hub.io/status/valr_0.5.0.9000.tar.gz-2563a7c26854498881687805cb91978a

commented

I can't get the rhub check to run cleanly. Are you confident the rchk error is fixed with last patch?

commented

Pretty sure, but I'll rerun the checks and link the build reports to show that the error caught by CRANs rchk is resolved.

commented

Here are the relevant errors that are caught with valr prior to fix (8f88e64). Full build report

Function init_factor(SEXPREC*, SEXPREC*)
  [UP] unprotected variable factor_string while calling allocating function Rf_setAttrib(?,S:levels,?) /opt/R-svn/packages/build/0EoR751h/valr/src/valr_utils.cpp:23

Function rowwise_subset_df(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage> const&, Rcpp::Vector<13, Rcpp::PreserveStorage>, bool)
  [UP] calling allocating function init_factor(SEXPREC*, SEXPREC*) with a fresh pointer (levels <arg 2>) /opt/R-svn/packages/build/0EoR751h/valr/src/valr_utils.cpp:109

Function rowwise_subset_df(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage> const&, std::__1::vector<int, std::__1::allocator<int> >, bool)
  [UP] calling allocating function init_factor(SEXPREC*, SEXPREC*) with a fresh pointer (levels <arg 2>) /opt/R-svn/packages/build/0EoR751h/valr/src/valr_utils.cpp:207

With the fix on current master, these errors are not reported (build report)

Note that there are some other "errors" reported, including some from Rcpp, however these are likely false alarms. The cran rchk report is filtered to include only those errors that are likely real (see kalibera/rchk#16). So we are following best practices as far as I can tell.