From 63c1bf754306d77c109b25406638c2b60099e8c6 Mon Sep 17 00:00:00 2001 From: Derek Ogle Date: Wed, 1 Feb 2023 11:06:53 -0600 Subject: [PATCH 1/3] Initiating v0.9.4.9000 --- DESCRIPTION | 2 +- NEWS.md | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b20c7b94..ed5b90e2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: FSA -Version: 0.9.4 +Version: 0.9.4.9000 Date: 2023-2-1 Title: Simple Fisheries Stock Assessment Methods Description: A variety of simple fish stock assessment methods. diff --git a/NEWS.md b/NEWS.md index cb73bd7a..f59bcc06 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +# FSA 0.9.4.9000 + + # FSA 0.9.4 * Changes related to moving to fishR-Core-Team * Updated sticker. From f3d09d047d86a443e1722c4e3a3e54b2e00999ce Mon Sep 17 00:00:00 2001 From: Derek Ogle Date: Thu, 24 Aug 2023 10:21:20 -0500 Subject: [PATCH 2/3] Update release-prep-template.md --- .github/ISSUE_TEMPLATE/release-prep-template.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/release-prep-template.md b/.github/ISSUE_TEMPLATE/release-prep-template.md index 689f37fe..eb9cbb0d 100644 --- a/.github/ISSUE_TEMPLATE/release-prep-template.md +++ b/.github/ISSUE_TEMPLATE/release-prep-template.md @@ -8,7 +8,7 @@ assignees: '' --- -Below are the steps used to prepare `FSAdata` for submission to CRAN. 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). +Below are the steps used to prepare `FSA` for submission to CRAN. 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. @@ -20,7 +20,7 @@ It is worth noting that this whole process can take 2-3 hours (or more depending - [ ] 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](https://cran.r-project.org/web/checks/check_results_FSAdata.html) +- [ ] Ensure no outstanding issues in [checks on CRAN](https://cran.r-project.org/web/checks/check_results_FSA.html) - [ ] 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**. @@ -38,7 +38,7 @@ It is worth noting that this whole process can take 2-3 hours (or more depending ### 3 - `dev` branch (at remote GitHub repo) - [ ] Ensure that "R-CMD-check.yaml" [GitHub action](https://github.com/fishR-Core-Team/FSA/actions) 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.*] +- [ ] Create a pull-request asking to merge the `dev` branch to the `main` branch. Ask someone from the FSA 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. @@ -53,11 +53,11 @@ It is worth noting that this whole process can take 2-3 hours (or more depending - [ ] 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](https://github.com/fishR-Core-Team/FSAdata/releases). `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`. +- [ ] Create a [new release](https://github.com/fishR-Core-Team/FSA/releases). `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.* +- [ ] Merge pull request from `main` branch (*OK to do this without getting approval from FSA 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. From a24a51edb06b69580af28c10a01f8ee4b6ccaf27 Mon Sep 17 00:00:00 2001 From: Derek Ogle Date: Fri, 25 Aug 2023 18:52:28 -0500 Subject: [PATCH 3/3] Prepping v0.9.5 --- DESCRIPTION | 4 +- NEWS.md | 4 +- R/FSA.R | 5 +- cran-comments/cran-comments-v0_9_5.md | 10 + docs/LICENSE-text.html | 2 +- docs/authors.html | 6 +- docs/index.html | 2 +- docs/news/index.html | 35 ++- docs/pkgdown.yml | 4 +- docs/reference/BluegillJL.html | 2 +- docs/reference/BrookTroutTH.html | 2 +- docs/reference/ChinookArg.html | 2 +- docs/reference/CodNorwegian.html | 2 +- docs/reference/CutthroatAL.html | 2 +- docs/reference/Ecoli.html | 2 +- docs/reference/FSA-internals.html | 2 +- docs/reference/FSA.html | 2 +- docs/reference/Mirex.html | 2 +- docs/reference/PSDlit.html | 16 +- docs/reference/PikeNY.html | 2 +- docs/reference/PikeNYPartial1.html | 2 +- docs/reference/SMBassLS.html | 2 +- docs/reference/SMBassWB.html | 2 +- docs/reference/Schnute-1.png | Bin 11226 -> 11239 bytes docs/reference/Schnute.html | 2 +- docs/reference/SpotVA1.html | 2 +- docs/reference/Summarize.html | 2 +- docs/reference/WR79.html | 2 +- docs/reference/WSlit.html | 4 +- docs/reference/WhitefishLC.html | 2 +- docs/reference/addZeroCatch.html | 2 +- docs/reference/ageBias.html | 2 +- docs/reference/agePrecision.html | 2 +- docs/reference/alkAgeDist.html | 2 +- docs/reference/alkIndivAge.html | 60 ++--- docs/reference/alkMeanVar.html | 2 +- docs/reference/alkPlot.html | 2 +- docs/reference/binCI.html | 2 +- docs/reference/capHistConvert.html | 2 +- docs/reference/capHistSum.html | 2 +- docs/reference/catchCurve.html | 2 +- docs/reference/chapmanRobson.html | 2 +- docs/reference/col2rgbt.html | 2 +- docs/reference/depletion.html | 2 +- docs/reference/dunnTest.html | 2 +- docs/reference/expandCounts.html | 124 ++++----- docs/reference/expandLenFreq.html | 2 +- docs/reference/extraTests.html | 2 +- docs/reference/fact2num.html | 2 +- docs/reference/fishR.html | 2 +- docs/reference/geomean.html | 2 +- docs/reference/growthModels.html | 354 +++++++++++++++----------- docs/reference/headtail.html | 2 +- docs/reference/hist.formula.html | 2 +- docs/reference/histFromSum.html | 2 +- docs/reference/hyperCI.html | 2 +- docs/reference/index.html | 2 +- docs/reference/knitUtil.html | 2 +- docs/reference/ksTest.html | 2 +- docs/reference/lagratio.html | 2 +- docs/reference/lencat.html | 2 +- docs/reference/logbtcf.html | 2 +- docs/reference/lwCompPreds.html | 2 +- docs/reference/metaM.html | 2 +- docs/reference/mrClosed.html | 2 +- docs/reference/mrOpen.html | 2 +- docs/reference/nlsBoot.html | 2 +- docs/reference/nlsTracePlot.html | 2 +- docs/reference/perc.html | 2 +- docs/reference/plotAB.html | 2 +- docs/reference/poiCI.html | 2 +- docs/reference/psdAdd.html | 2 +- docs/reference/psdCI.html | 2 +- docs/reference/psdCalc.html | 24 +- docs/reference/psdPlot.html | 2 +- docs/reference/psdVal.html | 33 +-- docs/reference/rSquared.html | 2 +- docs/reference/rcumsum.html | 2 +- docs/reference/removal.html | 2 +- docs/reference/se.html | 2 +- docs/reference/srStarts.html | 2 +- docs/reference/sumTable.html | 2 +- docs/reference/tictactoe.html | 2 +- docs/reference/validn.html | 2 +- docs/reference/vbStarts.html | 2 +- docs/reference/wrAdd.html | 2 +- docs/reference/wsVal.html | 47 ++-- man/FSA.Rd | 21 ++ 88 files changed, 499 insertions(+), 394 deletions(-) create mode 100644 cran-comments/cran-comments-v0_9_5.md diff --git a/DESCRIPTION b/DESCRIPTION index ed5b90e2..0a97d508 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FSA -Version: 0.9.4.9000 -Date: 2023-2-1 +Version: 0.9.5 +Date: 2023-8-25 Title: Simple Fisheries Stock Assessment Methods Description: A variety of simple fish stock assessment methods. Authors@R: c( diff --git a/NEWS.md b/NEWS.md index f59bcc06..1df696df 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# FSA 0.9.4.9000 - +# FSA 0.9.5 +* Fixed FSA-package \alias problem using the "automatic approach" (i.e., adding a "_PACKAGE" line to FSA.R) suggested in an e-mail from Kurt Hornik on 19-Aug-2023. # FSA 0.9.4 * Changes related to moving to fishR-Core-Team diff --git a/R/FSA.R b/R/FSA.R index 08c679c9..01c9ed80 100644 --- a/R/FSA.R +++ b/R/FSA.R @@ -15,8 +15,9 @@ #' #' @references Ogle, D.H. 2016. \href{https://fishr-core-team.github.io/fishR/pages/books.html#introductory-fisheries-analyses-with-r}{Introductory Fisheries Analyses with R}. Chapman & Hall/CRC, Boca Raton, FL. #' -#' @docType package -#' #' @name FSA #' +#' @keywords internal +"_PACKAGE" + NULL \ No newline at end of file diff --git a/cran-comments/cran-comments-v0_9_5.md b/cran-comments/cran-comments-v0_9_5.md new file mode 100644 index 00000000..bdf104f7 --- /dev/null +++ b/cran-comments/cran-comments-v0_9_5.md @@ -0,0 +1,10 @@ +* This updates the existing FSA package on CRAN with minor fixes and correction for package alias per e-mail from Kurt Hornik on 19-Aug-23. + +## Notes +* There may be a note about "fishR" being misspelled in the description. This is not a misspelling. + +## Testing Environments +* My Windows machine. +* Win Builder -- old-release, release, and development. +* Mac Builder +* GitHub Action (R-CMD-check.yaml) diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 982fc39e..8ccb22af 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -10,7 +10,7 @@ FSA - 0.9.4 + 0.9.5