fishr-core-team / fsadata Goto Github PK

Below are the steps that I used when preparing FSAdata v0.4.1 for submission to CRAN. This process can be followed for future releases.

The steps should generally be followed in order (i.e., don't move to the next step without success at the current step). It is common to have to repeat some previous steps if an error/warning occurs at a subsequent step (in my experience, this most often happens after checking on the development version of R when using R-winbuilder).

It is worth noting that this whole process can take 2-3 hours (or more depending on internet speed) with significant "waiting time" for checks and builds.

0 - Preparatory Updates

• Update to latest R version.
• Update to latest RStudio version.
• Update all packages, especially those that FSA and FSAdata depend on.

1 - dev branch (at local repo)

• Ensure no outstanding issues in checks on CRAN
• Ensure that all branches emanating from dev have been appropriately merged to dev via pull request.
• Update Version field in DESCRIPTION (next number up without the .9000 on the end).
• Update Date field in DESCRIPTION.
• Update Version in top header of NEWS.md (next number up without the .9000 on the end).
• Ensure that NEWS.md contains descriptions of all major changes (this is usually done in "real-time" as changes are being made).
• Create new cran-comments-vX_X_X.md file in cran-comments folder. This will likely just be a copy of the same file from the previous version, but may include notes specific to inquiries from CRAN operators. [Note that this will be used in Section 5 below, so leave the file open).
• Run pkgdown::build_site() in the console of RStudio.

2 - dev branch (at local repo)

• Run Build..Check in RStudio. Address all errors, warnings, and notes and redo parts of the previous section as necessary. [There should generally be no errors, warnings, or notes as the package should have been checked with each major change to dev. At times I will get a note about a new author or not being able to verify current time.]
• Build a "source package" in RStudio with More..Build Source Package.
• Upload source package to all three "flavors" at R-winbuilder. Wait for an e-mail reply from R-winbuilder. Any errors, warnings, or notes for any flavor should be addressed (after which this step, and possibly relevant steps above, should be repeated).
• Upload source package to both the "release" and "development" "flavors" at R-macbuilder. Monitor results (especially "Check Log") page (will be given a link upon submission). Any errors, warnings, or notes for any flavor should be addressed (after which this step, and possibly relevant steps above, should be repeated).
• Push changes from above from local machine to dev branch on GitHub.

3 - dev branch (at remote GitHub repo)

• Ensure that "R-CMD-check.yaml" GitHub action was successful for the dev branch (this should run automatically with the push to dev, but will take some time to finish (possibly >20 mins)). If not successful then address issues and repeat as much above as necessary.
• Create a pull-request asking to merge the dev branch to the main branch. Ask someone from the FSAdata team to review the request. [Ensure that all checks were successfully completed.]

4 - main branch (at remote GitHub repo)

• Merge approved (assumingly) pull request from dev branch.

5 - main branch (at local repo)

• Fetch the remote main branch and pull the updates to local main branch so that the local and remote main branches are the same.
• Build a "source package" in RStudio with More..Build Source Package.
• Build a "binary package" in RStudio with More..Build Binary Package.
• Goto the CRAN submission page. Enter your first and last names. Press Choose File and choose the source file (.tar.gz) created above. Copy the comments from the relevant cran-comments-vX_X_X.md and paste into the optional comments box. Press the Upload Package button.
• Review the ensuing page (it is usually correct) and press Submit Package button at the bottom.
• Wait for an e-mail from CRAN (this is usually pretty quick) and press the contained link to open a new webpage.
• Check all three boxes (make sure that your answers are truthful) and press Upload the Package to CRAN. You should get a confirmation e-mail almost immediately (no need to respond to this).

6 - main branch (at remote GitHub repo)

• Create a new release. Tag should relate to the version number and the Title should state that the version number is being released to CRAN (see past examples). Make sure that the Target is set to Main. Add an optional Description if desired. Drag and drop the source (.tar.gz) and binary (.zip) files created in the previous step on to the Attach binaries ... box. Press Publish Release.

7 - dev branch (at remote GitHub repo)

• Create a pull-request asking to merge the main branch to the dev branch. This is needed after merging dev to main above so that the two branches are synced.
• Merge pull request from main branch (OK to do this without getting approval from FSAdata team member). Note that the dev branch will say it is "1 commit ahead of main" after this step.

8 - dev branch (at local repo)

• Fetch the remote dev branch and pull the updates to local dev branch so that the local and remote dev branches are the same.
• Update Version field in DESCRIPTION by appending .9000 to the end.
• Create a new section at the top of NEWS.md with the new version number (i.e., including the .9000 on the end).
• Push these changes to the remote dev branch. This is the start of the next version.

"tl in mm" should be "tl in inch"

A CRAN note (for v0.3.9) indicates that there is an undeclared reference to the FSA package in the documentation. I think that this is likely in SpotVA2. I think that this note can be corrected by either putting FSA as a suggests: in the DESCRIPTION file or removing the link to FSA in SpotVA2 (it is not that important to link that documentation to the documentation for SpotVA1 in FSA ... and several versions ago I tried to remove all of these links as they were largely a pain).

If we go with the latter then I would change this text in SpotVA2.R

from the \code{\link[FSA]{SpotVA1}} data frame were

to

from the \code{SpotVA1} data frame in \pkg{FSA} were

Otolith-Data.xlsx
Glossogobius aureus, Philippines

Consider using the fryingpane function to serve the data files in the RStudio Connections pane. See fryingpane here.

The following items should be changed, modified, or corrected following the transfer of the repo to fishrR-Core-Team.

• Change the ReadMe
  • Remove references to Derek,
  • Correct links to FSA (once it has been transferred)
  • Correct link to fishR webpage (once that is at AFS)
• Start a new .9000 version.
• Start a new "ongoing" section in the NEWS
• Setup codecov.
• Transfer. update, or setup the Zenodo DOI.
• Determine team member access (see Settings ... Collaborators and teams)
• Make sure the RCMD-CHECK Action works
• Reconsider the license type (complete descriptions, summarized, help choosing)

Add more items as we think of them.

Those on fishR-Core-Team should update our remote link to FSAdata or checkout a new local copy if we had a local copy from droglenc.

Fold in the data files from the Introductory Fisheries Analysis with R book that were not already in FSAdata.

I found errors in the following datasets (or, rather, in the accompanying documentation):
RWhitefishAI Ages and lengths of Round Whitefish.
RWhitefishIR Ages and lengths of Round Whitefish.

• Typo in the scientific name: Prosopium cylindraecum -> cylindraceum
• TL is in inch, not cm

Determine if there is a good way to insert special characters, e.g., as in non-Americanized names, into RD files.

Either make a vignette or modify Readme.md to include a list of data.frames by topic. Basically a static version of the help.search() described in ?FSAdata.