Release v2.2.2

[gothub]

• [x] close any issues assigned to this release
• [x] check and update contributors list and update DESCRIPTION/CITATION if needed
• [x] Update version number, publish date, etc. in DESCRIPTION
• [x] check that all new functions have unit tests
• [x] update NEWS
• [x] update cran_comments
• [x] run revdepcheck::revdep_check()
• [x] run tests with cran=true and network cable unplugged
  • devtools::check(vignettes = FALSE, env_vars = c(NOT_CRAN = "false"))
• [x] test with testthat 3e
• [x] devtools::check(remote=TRUE, cran=TRUE)
  • [x] macOS
  • [x] Ubuntu
• [x] win-builder
  • [x] devtools::check_win_devel()
  • [x] devtools::check_win_devel()
  • [x] devtools::check_win_old_release()
• [x] devtools::check() with valid "stage" environment token
• [x] rhub::check_for_cran(email = "jclark@nceas.ucsb.edu", platforms = c("debian-gcc-devel", "fedora-clang-devel", "fedora-gcc-devel", "macos-m1-bigsur-release", "macos-highsierra-release-cran", "windows-x86_64-devel", "windows-x86_64-release"))
  • [ ] debian-gcc-devel (Debian Linux, R-devel)
  • [x] fedora-clang-devel (Fedora Linux, R-devel, clang, gfortran)
  • [x] fedora-gcc-devel (Fedora Linux, R-devel, GCC)
  • [x] macos-m1-bigsur-release (Apple Silicon (M1), macOS 11.6 Big Sur, R-release)
  • [x] macos-highsierra-release-cran (macOS 10.13.6 High Sierra, R-release, CRAN's setup)
  • [x] windows-x86_64-devel (Windows Server 2008 R2 SP1, R-devel, 32/64 bit)
  • [x] windows-x86_64-release (Windows Server 2008 R2 SP1, R-release, 32/64 bit)
• [x] run spell_check()
• [x] merge develop into main
• [x] run devtools::release() After release is posted by CRAN:
• [x] create release tag
• [ ] update package revision (in 'develop' branch) to development version i.e. 2.2.2.9000

[jeanetteclark]

All tests are passing except for rhub with Debian because of setup issues - for some reason its installing some packages from bioconductor? I'm not sure.

[jeanetteclark]

@mbjones this is ready for review

[jeanetteclark]

re: rhub testing I got the following results

• windows-devel

Found the following files/directories:
  'lastMiKTeXException'

• windows-release

Maintainer: 'Matthew B. Jones <[jones@nceas.ucsb.edu](mailto:jones@nceas.ucsb.edu)>'

  URL: https://cilogon.org/?skin=DataONE
Found the following (possibly) invalid URLs:
          man/MNode-class.Rd
    From: man/AuthenticationManager-class.Rd
          man/createObject.Rd
          man/archive.Rd
          man/generateIdentifier.Rd
          man/setObsoletedBy.Rd
          man/updateObject.Rd
          man/updateSystemMetadata.Rd
    Status: Error
    Message: libcurl error code 35:
        schannel: next InitializeSecurityContext failed: SEC_E_ILLEGAL_MESSAGE (0x80090326) - This error usually occurs when a fatal SSL/TLS alert is received (e.g. handshake failed).

• debian-devel

 149#> Downloading GitHub repo r-lib/remotes@r-hub
 150#> Running `R CMD build`...
 151#> * checking for file ‘/tmp/RtmpnPOnPV/remotes63577b721e/r-lib-remotes-6e26f33/DESCRIPTION’ ... OK
 152#> * preparing ‘remotes’:
 153#> * checking DESCRIPTION meta-information ... OK
 154#> * checking for LF line-endings in source and make files and shell scripts
 155#> * checking for empty or unneeded directories
 156#> * building ‘remotes_2.1.1.9000.tar.gz’
 157#> Installing package into ‘/home/docker/R’
 158#> (as ‘lib’ is unspecified)
 159#> Error : Bioconductor does not yet build and check packages for R version 4.3; see
 160#> https://bioconductor.org/install

[jeanetteclark]

since the debian issue and the two windows issues seem specific to rhub I'm going to merge and release this