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Merge pull request #537 from OuhscBbmc/dev
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prep for v1.2.0
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@wibeasley
wibeasley authored Sep 7, 2024
2 parents 9f2b424 + 6b31ad6 commit 14feb11
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2 changes: 1 addition & 1 deletion NEWS.md
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Expand Up @@ -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")`
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2 changes: 1 addition & 1 deletion R/retrieve-credential.R
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Expand Up @@ -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.
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62 changes: 32 additions & 30 deletions cran-comments.md
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Expand Up @@ -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:
<https://github.com/RaymondBalise/tidyREDCap/pull/61>.

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: <https://github.com/OuhscBbmc/REDCapR/blob/main/revdep/cran.md>
2 changes: 1 addition & 1 deletion man/retrieve_credential.Rd
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96 changes: 48 additions & 48 deletions revdep/README.md
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Expand Up @@ -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

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22 changes: 11 additions & 11 deletions revdep/problems.md
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Expand Up @@ -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) `<fn>`()
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) `<fn>`()
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
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6 changes: 3 additions & 3 deletions utility/refresh.R
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Expand Up @@ -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="[email protected]")
# devtools::check_win_devel() # CRAN submission policies encourage the development version
# revdepcheck::revdep_check(num_workers = 4)
# Check Rhub at <https://github.com/OuhscBbmc/REDCapR/actions/workflows/rhub.yaml>
# Check reverse dependencies at <https://github.com/OuhscBbmc/REDCapR/actions/workflows/recheck.yml>
# 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.
2 changes: 1 addition & 1 deletion vignettes/TroubleshootingApiCalls.Rmd
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Expand Up @@ -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

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