diff --git a/NEWS.md b/NEWS.md index 7b45511f..9cc9f69d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -8,7 +8,7 @@ Quick links: * [Current & previous GitHub Issues](https://github.com/OuhscBbmc/REDCapR/issues?q=is%3Aissue) * [Documentation for current GitHub version](https://ouhscbbmc.github.io/REDCapR/) -Upcoming Changes in v1.2.0 +Version 1.2.0 (released 2024-09-08) ========================================================== These features are not yet on CRAN. Install with `remotes::install_github("OuhscBbmc/REDCapR")` diff --git a/R/retrieve-credential.R b/R/retrieve-credential.R index 4d70b09b..c9c738b7 100644 --- a/R/retrieve-credential.R +++ b/R/retrieve-credential.R @@ -78,7 +78,7 @@ #' Follow these steps to adapt to your desired REDCap project(s): #' 1. Modify the credential file for the REDCap API with a text editor #' like [Notepad++](https://notepad-plus-plus.org/), -#' [Visual Studio Code](https://code.visualstudio.com), or +#' Visual Studio Code, or #' [nano](https://www.nano-editor.org/). #' Replace existing records with the information from your projects. #' Delete the remaining example records. diff --git a/cran-comments.md b/cran-comments.md index 15bd31ea..e487596d 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -11,51 +11,53 @@ Test environments 1. Local Ubuntu, R 4.4.1 2. Local Win11, R 4.4.1 patched 3. R-hub - 1. [Ubuntu Linux, R-release, GCC](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-6f45462d131a4ac49833c0c7c014bad0) - 2. [Fedora Linux, R-devel, clang, gfortran](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-2e9560e6fcdb4467af8e9ea8d22c165d) - 3. [Windows Server](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-3ec1ed8fac734d24a16cc5ecf238cf47) -4. [win-builder](https://win-builder.r-project.org/N3n87tj2ky0v/), development version. -5. [GiHub Actions](https://github.com/OuhscBbmc/REDCapR/actions), Ubuntu 22.04 LTS + 1. [Ubuntu Linux, R-devel](https://github.com/OuhscBbmc/REDCapR/actions/runs/10748844649/job/29817754743) + 2. [Windows Server, R-devel](https://github.com/OuhscBbmc/REDCapR/actions/runs/10748844649/job/29817754878) + 3. [MacOS, R-devel](https://github.com/OuhscBbmc/REDCapR/actions/runs/10748844649/job/29817754969) +4. [win-builder](https://win-builder.r-project.org/6a44Y48qLSlw/), development version. +5. [GiHub Actions R-CMD-check](https://github.com/OuhscBbmc/REDCapR/actions/workflows/check-release.yaml), Ubuntu 22.04 LTS R CMD check results ----------------------------------------------- * No ERRORs or WARNINGs on any builds. - -* There are two NOTEs across the R-hub builds: - - ```txt - * checking for detritus in the temp directory ... NOTE - Found the following files/directories: - 'lastMiKTeXException' +* One one Ubuntu build, there was this warning. + I don't understand the source. I'm not calling any function called `tidy()` when I search. And the two hyperlinks containing "tidy" look fine to my eye. + ``` - As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this could be due to a bug/crash in MiKTeX and can likely be ignored. - - ```txt - * checking HTML version of manual ... NOTE + ❯ checking HTML version of manual ... NOTE Skipping checking HTML validation: no command 'tidy' found ``` - Based on [this discussion](https://groups.google.com/g/r-sig-mac/c/7u_ivEj4zhM?pli=1) - and [this SO answer](https://stackoverflow.com/a/75007979/1082435), - it sounds like a problem with the testing environment and not the package code. - Downstream dependencies ----------------------------------------------- With one exception, -packages that depend/import/suggest REDCapR pass checks with `revdepcheck::revdep_check()`. +packages that depend/import/suggest REDCapR pass the +[Reverse dependency check](https://github.com/OuhscBbmc/REDCapR/actions/workflows/recheck.yml)s. I worked with **tidyREDCap** team and they accepted a PR that fixes the problem: . - -package | E | W | N -------- | - | - | - -codified 0.3.0 | E: 0 | W: 0 | N: 0 -REDCapDM 0.7.0 | E: 0 | W: 0 | N: 1 -REDCapCAST 23.6.2 | E: 0 | W: 0 | N: 0 -REDCapTidieR 0.4.0 | E: 1 | W: 0 | N: 0 -tidyREDCap 1.1.1 | E: 0 +1 | W: 0 | N: 0 -ReviewR 2.3.8 | E: 0 | W: 0 | N: 1 +It completes successfully on my local machine. + +``` +------- Check results summary ------ +Check status summary: + ERROR NOTE OK + Source packages 0 0 1 + Reverse depends 1 2 3 + +Check results summary: +REDCapR ... OK +rdepends_REDCapCAST ... OK +rdepends_REDCapDM ... NOTE +* checking data for non-ASCII characters ... NOTE +rdepends_REDCapTidieR ... OK +rdepends_ReviewR ... NOTE +* checking data for non-ASCII characters ... NOTE +rdepends_codified ... OK +rdepends_tidyREDCap ... ERROR +* checking tests ... ERROR +``` Results: diff --git a/man/retrieve_credential.Rd b/man/retrieve_credential.Rd index f6c4f00d..1dfad026 100644 --- a/man/retrieve_credential.Rd +++ b/man/retrieve_credential.Rd @@ -89,7 +89,7 @@ Follow these steps to adapt to your desired REDCap project(s): \enumerate{ \item Modify the credential file for the REDCap API with a text editor like \href{https://notepad-plus-plus.org/}{Notepad++}, -\href{https://code.visualstudio.com}{Visual Studio Code}, or +Visual Studio Code, or \href{https://www.nano-editor.org/}{nano}. Replace existing records with the information from your projects. Delete the remaining example records. diff --git a/revdep/README.md b/revdep/README.md index 96955a01..f165634c 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,63 +2,63 @@ |field |value | |:--------|:------------------------------------------------| -|version |R version 4.3.1 Patched (2023-07-06 r84647 ucrt) | -|os |Windows 11 x64 (build 22621) | +|version |R version 4.4.1 Patched (2024-08-05 r86990 ucrt) | +|os |Windows 10 x64 (build 19045) | |system |x86_64, mingw32 | |ui |RStudio | |language |(EN) | |collate |English_United States.utf8 | |ctype |English_United States.utf8 | |tz |America/Chicago | -|date |2023-09-04 | -|rstudio |2023.06.1+524 Mountain Hydrangea (desktop) | -|pandoc |3.1.5 @ C:\PROGRA~1\Pandoc\pandoc.exe | +|date |2024-09-07 | +|rstudio |2024.04.2+764 Chocolate Cosmos (desktop) | +|pandoc |2.5 @ C:\PROGRA~2\Pandoc\pandoc.exe | # Dependencies -|package |old |new |Δ | -|:-----------|:------|:--------|:--| -|REDCapR |1.1.0 |1.1.9005 |* | -|askpass |1.2.0 |1.2.0 | | -|backports |1.4.1 |1.4.1 | | -|bit |4.0.5 |4.0.5 | | -|bit64 |4.0.5 |4.0.5 | | -|checkmate |2.2.0 |2.2.0 | | -|cli |3.6.1 |3.6.1 | | -|clipr |0.8.0 |0.8.0 | | -|cpp11 |0.4.6 |0.4.6 | | -|crayon |1.5.2 |1.5.2 | | -|curl |5.0.2 |5.0.2 | | -|dplyr |1.1.3 |1.1.3 | | -|fansi |1.0.4 |1.0.4 | | -|generics |0.1.3 |0.1.3 | | -|glue |1.6.2 |1.6.2 | | -|hms |1.1.3 |1.1.3 | | -|httr |1.4.7 |1.4.7 | | -|jsonlite |1.8.7 |1.8.7 | | -|lifecycle |1.0.3 |1.0.3 | | -|magrittr |2.0.3 |2.0.3 | | -|mime |0.12 |0.12 | | -|openssl |2.1.0 |2.1.0 | | -|pillar |1.9.0 |1.9.0 | | -|pkgconfig |2.0.3 |2.0.3 | | -|prettyunits |1.1.1 |1.1.1 | | -|progress |1.2.2 |1.2.2 | | -|purrr |1.0.2 |1.0.2 | | -|R6 |2.5.1 |2.5.1 | | -|readr |2.1.4 |2.1.4 | | -|rlang |1.1.1 |1.1.1 | | -|stringi |1.7.12 |1.7.12 | | -|stringr |1.5.0 |1.5.0 | | -|sys |3.4.2 |3.4.2 | | -|tibble |3.2.1 |3.2.1 | | -|tidyr |1.3.0 |1.3.0 | | -|tidyselect |1.2.0 |1.2.0 | | -|tzdb |0.4.0 |0.4.0 | | -|utf8 |1.2.3 |1.2.3 | | -|vctrs |0.6.3 |0.6.3 | | -|vroom |1.6.3 |1.6.3 | | -|withr |2.5.0 |2.5.0 | | +|package |old |new |Δ | +|:-----------|:-----|:--------|:--| +|REDCapR |1.1.0 |1.1.9007 |* | +|askpass |1.2.0 |1.2.0 | | +|backports |1.5.0 |1.5.0 | | +|bit |4.0.5 |4.0.5 | | +|bit64 |4.0.5 |4.0.5 | | +|checkmate |2.3.2 |2.3.2 | | +|cli |3.6.3 |3.6.3 | | +|clipr |0.8.0 |0.8.0 | | +|cpp11 |0.5.0 |0.5.0 | | +|crayon |1.5.3 |1.5.3 | | +|curl |5.2.2 |5.2.2 | | +|dplyr |1.1.4 |1.1.4 | | +|fansi |1.0.6 |1.0.6 | | +|generics |0.1.3 |0.1.3 | | +|glue |1.7.0 |1.7.0 | | +|hms |1.1.3 |1.1.3 | | +|httr |1.4.7 |1.4.7 | | +|jsonlite |1.8.8 |1.8.8 | | +|lifecycle |1.0.4 |1.0.4 | | +|magrittr |2.0.3 |2.0.3 | | +|mime |0.12 |0.12 | | +|openssl |2.2.1 |2.2.1 | | +|pillar |1.9.0 |1.9.0 | | +|pkgconfig |2.0.3 |2.0.3 | | +|prettyunits |1.2.0 |1.2.0 | | +|progress |1.2.3 |1.2.3 | | +|purrr |1.0.2 |1.0.2 | | +|R6 |2.5.1 |2.5.1 | | +|readr |2.1.5 |2.1.5 | | +|rlang |1.1.4 |1.1.4 | | +|stringi |1.8.4 |1.8.4 | | +|stringr |1.5.1 |1.5.1 | | +|sys |3.4.2 |3.4.2 | | +|tibble |3.2.1 |3.2.1 | | +|tidyr |1.3.1 |1.3.1 | | +|tidyselect |1.2.1 |1.2.1 | | +|tzdb |0.4.0 |0.4.0 | | +|utf8 |1.2.4 |1.2.4 | | +|vctrs |0.6.5 |0.6.5 | | +|vroom |1.6.5 |1.6.5 | | +|withr |3.0.1 |3.0.1 | | # Revdeps diff --git a/revdep/problems.md b/revdep/problems.md index 0ddeaf2c..aa9dcdc5 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -20,17 +20,17 @@ Run `revdepcheck::revdep_details(, "tidyREDCap")` for more info ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: - 8. │ └─rlang::try_fetch(...) - 9. │ └─base::withCallingHandlers(...) - 10. └─tidyselect:::vars_select_eval(...) - 11. └─tidyselect:::ensure_named(...) - 12. └─vctrs::vec_as_names(names(pos), repair = "check_unique", call = call) - 13. └─vctrs (local) ``() - 14. └─vctrs:::validate_unique(names = names, arg = arg, call = call) - 15. └─vctrs:::stop_names_must_be_unique(names, arg, call = call) - 16. └─vctrs:::stop_names(...) - 17. └─vctrs:::stop_vctrs(...) - 18. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) + 7. ├─tidyselect:::with_subscript_errors(...) + 8. │ └─base::withCallingHandlers(...) + 9. └─tidyselect:::vars_select_eval(...) + 10. └─tidyselect:::ensure_named(...) + 11. └─vctrs::vec_as_names(names(pos), repair = "check_unique", call = call) + 12. └─vctrs (local) ``() + 13. └─vctrs:::validate_unique(names = names, arg = arg, call = call) + 14. └─vctrs:::stop_names_must_be_unique(names, arg, call = call) + 15. └─vctrs:::stop_names(...) + 16. └─vctrs:::stop_vctrs(...) + 17. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) [ FAIL 1 | WARN 8 | SKIP 0 | PASS 13 ] Error: Test failures diff --git a/utility/refresh.R b/utility/refresh.R index 3b8da506..f317d1fc 100644 --- a/utility/refresh.R +++ b/utility/refresh.R @@ -56,9 +56,9 @@ devtools::check( # Equivalent of R-hub remote = TRUE, incoming = TRUE ) -rhub::list_validated_emails(); # rhub::validate_email() -rhub::check_for_cran(email="wibeasley@hotmail.com") # devtools::check_win_devel() # CRAN submission policies encourage the development version -# revdepcheck::revdep_check(num_workers = 4) +# Check Rhub at +# Check reverse dependencies at +# Old way: revdepcheck::revdep_check(num_workers = 4) # usethis::use_release_issue() # devtools::release(check=FALSE) #Careful, the last question ultimately uploads it to CRAN, where you can't delete/reverse your decision. diff --git a/vignettes/TroubleshootingApiCalls.Rmd b/vignettes/TroubleshootingApiCalls.Rmd index 5e96677a..3f4ee30d 100644 --- a/vignettes/TroubleshootingApiCalls.Rmd +++ b/vignettes/TroubleshootingApiCalls.Rmd @@ -167,7 +167,7 @@ If one of these checks fail, please start by consulting your REDCap administrato Common Gotchas {#gotchas-agnostic} ------------------------------------------------------------------ -1. **Problems in the project's metadata/dictionary.** If exporting the metadata fails (*e.g.*, [`REDCapR::redcap_metadata_read()`](https://ouhscbbmc.github.io/REDCapR/reference/redcap_metadata_read.html) and [`redcapAPI::exportMetaData()`](https://www.rdocumentation.org/packages/redcapAPI/versions/2.0/topics/exportMetaData.html)), manually download the data dictionary from the REDCap browser. Inspect the plain text closely in a text editor like [Visual Studio Code](https://code.visualstudio.com); avoid programs like Excel that tend to interpret, align, and decorate the values, which sometimes masks problems. Scrutinize all elements, but especially look for nonstandard characters. *See the next bullet.* +1. **Problems in the project's metadata/dictionary.** If exporting the metadata fails (*e.g.*, [`REDCapR::redcap_metadata_read()`](https://ouhscbbmc.github.io/REDCapR/reference/redcap_metadata_read.html) and [`redcapAPI::exportMetaData()`](https://www.rdocumentation.org/packages/redcapAPI/versions/2.0/topics/exportMetaData.html)), manually download the data dictionary from the REDCap browser. Inspect the plain text closely in a text editor like Visual Studio Code; avoid programs like Excel that tend to interpret, align, and decorate the values, which sometimes masks problems. Scrutinize all elements, but especially look for nonstandard characters. *See the next bullet.* Some API libraries test that problematic elements of a project are handled correctly. If you encounter an element that causes problems, please consider