Release rsnps 0.6.1

[jooolia]

Prepare for release (working on dev branch):

• [x] git pull
• [x] Check current CRAN check results
• [x] Polish NEWS
  • add in issue numbers
• [x] devtools::build_readme()
• [x] urlchecker::url_check()
• [x] devtools::check(remote = TRUE, manual = TRUE)

── R CMD check results ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── rsnps 0.5.1 ────
Duration: 2m 12.7s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

• [x] devtools::check_win_devel()
  • ok - https://win-builder.r-project.org/G3s3tkejXQQB/
• [x] rhub::check_for_cran()
• [x] revdepcheck::revdep_check(num_workers = 4)

- ── INSTALL ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 2 versions ──
Installing CRAN version of rsnps
Installing DEV version of rsnps
── CHECK ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── 1 packages ──
[0/1] 00:10:05 | ETA:  ?s | (1) appreci8R [I]OK: 1
BROKEN: 0
Total time: 10 min

• [x] Update cran-comments.md

• [x] Update vignette by running vignettes/precompile.R.

• [x] update codemeta.json using codemetar::write_codemeta('.') (from within project folder on dev branch)

• [x] git push

• [x] Tag release

• [ ] Bump dev version

Submit to CRAN:

• [x] merge dev into master ~* [ ] usethis::use_version('patch')~
• [x] devtools::submit_cran()
• [x] Approve email

Wait for CRAN...

• [ ] Accepted :tada:
• [ ] git push
• [ ] usethis::use_github_release()
• [ ] usethis::use_dev_version()
• [ ] git push

[jooolia]

Apparently new release was not accepted because the resubmission did not have the release number incremented as stated in "Updates to previously-published packages must have an increased version. Increasing the version number at each submission reduces confusion so is preferred even when a previous submission was not accepted." https://cran.r-project.org/web/packages/policies.html Did not received any info about it being archived, only

"To: Julia Gustavsen j.gustavsen@gmail.com Cc: CRAN cran-submissions@r-project.org References: 20230630143816.77A03A024D@xmpalantir.wu.ac.at 3661e9e6-b63e-dc74-eeeb-b5b5656639a2@statistik.tu-dortmund.de CADcfdY=7E6j_Z-3CDU2jbOt0_4hjXXOYVfmN0PAER2P-8qcnSA@mail.gmail.com From: Uwe Ligges ligges@statistik.tu-dortmund.de Organization: Fakultät Statistik, Technische Universität Dortmund In-Reply-To: CADcfdY=7E6j_Z-3CDU2jbOt0_4hjXXOYVfmN0PAER2P-8qcnSA@mail.gmail.com Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit

Thanks, on its way to CRAN.

Best, Uwe Ligges "

[jooolia]

Will increment release number and resubmit again.

[jooolia]

Received mail from CRAN with things to fix

• [x] Please only single quote package and software names in your description and not every second word. #176

• [x] Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. #176

• [x] Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar)

• [x] Missing Rd-tags: ld_search-defunct.Rd: \value LDSearch-defunct.Rd: \value NCBI_snp_query-defunct.Rd: \value NCBI_snp_query2-defunct.Rd: \value tryget.Rd: \value. commit 71903d4

• [x] \dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please replace \dontrun with \donttest. #177

• [x] Please unwrap the examples if they are executable in < 5 sec, or replace dontrun{} with \donttest{}. #177

• [x] Please add small executable examples in your Rd-files to illustrate the use of the exported function but also enable automatic testing.

• [x] Some code lines in examples are commented out. Please never do that. #177

• [x] Ideally find toy examples that can be regularly executed and checked. Lengthy examples (> 5 sec), can be wrapped in \donttest{}.

• [x] Examples in comments in: read_users.Rd

• [x] Please fix and resubmit.

[jooolia]

Prepare for release (working on dev branch):

• [x] git pull
• [x] Check current CRAN check results
• [x] Polish NEWS
  • add in issue numbers
• [x] devtools::build_readme()
• [x] urlchecker::url_check()
• [x] devtools::check(remote = TRUE, manual = TRUE)

  
  ── R CMD check results ──────────────────────────────────────────────────────────────────────────────────── rsnps 0.6.2 ────
  Duration: 12m 51.6s

❯ checking CRAN incoming feasibility ... NOTE Maintainer: ‘Julia Gustavsen j.gustavsen@gmail.com’

New submission

Package was archived on CRAN

CRAN repository db overrides: X-CRAN-Comment: Archived on 2023-07-09 for policy violation.

On Internet access.

❯ checking top-level files ... NOTE Non-standard file/directory found at top level: ‘fix_cran.txt’

❯ checking examples ... NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed download_users 10.840 0.461 144.239 read_users 8.692 0.374 77.660 fetch_genotypes 4.838 0.286 72.649 users 3.958 0.221 68.745 allgensnp 3.116 0.033 296.299 ncbi_snp_query 0.643 0.040 13.008 allphenotypes 0.126 0.011 7.634

0 errors ✔ | 0 warnings ✔ | 3 notes ✖

* [ ] `devtools::check_win_devel()` 
* [ ] `rhub::check_for_cran()`
* ~[ ] `revdepcheck::revdep_check(num_workers = 4)`~ no longer on cran

* [ ] Update `cran-comments.md`

* [ ] Update vignette by running `vignettes/precompile.R`.
* [ ] update codemeta.json using `codemetar::write_codemeta('.')` (from within project folder on dev branch)
* [ ] `git push`
* [ ] Tag release
* [ ] Bump dev version

Submit to CRAN:
* []  merge dev into master
~* [ ] `usethis::use_version('patch')`~
* [ ] `devtools::submit_cran()`
* [ ] Approve email

Wait for CRAN...

* [ ] Accepted :tada:
* [ ] `git push`
* [ ] `usethis::use_github_release()`
* [ ] `usethis::use_dev_version()`
* [ ] `git push`