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updating revdepcheck notes
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@aylapear
aylapear committed Jan 22, 2025
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40 changes: 24 additions & 16 deletions revdep/README.md
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# Platform

|field |value |
|:--------|:-----------------------------------------------------------------------------------|
|version |R version 4.2.2 (2022-10-31) |
|os |macOS Ventura 13.0.1 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_CA.UTF-8 |
|ctype |en_CA.UTF-8 |
|tz |America/Vancouver |
|date |2022-12-16 |
|rstudio |2022.07.2+576 Spotted Wakerobin (desktop) |
|pandoc |2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown) |
|field |value |
|:--------|:-------------------------------------|
|version |R version 4.4.2 (2024-10-31) |
|os |macOS Sequoia 15.1.1 |
|system |aarch64, darwin20 |
|ui |RStudio |
|language |(EN) |
|collate |en_US.UTF-8 |
|ctype |en_US.UTF-8 |
|tz |America/Vancouver |
|date |2025-01-21 |
|rstudio |2024.12.0+467 Kousa Dogwood (desktop) |
|pandoc |NA |

# Dependencies

|package |old |new |Δ |
|:--------|:-----|:-----|:--|
|tidyplus |0.0.1 |0.0.2 |* |
|package |old |new |Δ |
|:--------|:----------|:------|:--|
|tidyplus |0.1.0.9003 |0.2.0 |* |
|chk |NA |0.10.0 |* |
|rlang |NA |1.1.4 |* |

# Revdeps

## New problems (1)

|package |version |error |warning |note |
|:---------|:----------|:-----|:-------|:-----------|
|[fwatlasbc](problems.md#fwatlasbc)|0.0.1.9018 |2 | |1 -1 __+1__ |

2 changes: 1 addition & 1 deletion revdep/cran.md
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## revdepcheck results

We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
We checked 2 reverse dependencies (0 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.

* We saw 0 new problems
* We failed to check 0 packages
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121 changes: 120 additions & 1 deletion revdep/problems.md
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*Wow, no problems at all. :)*
# fwatlasbc

<details>

* Version: 0.0.1.9018
* GitHub: NA
* Source code: https://github.com/cran/fwatlasbc
* Number of recursive dependencies: 131

Run `revdepcheck::revdep_details(, "fwatlasbc")` for more info

</details>

## Newly broken

* checking dependencies in R code ...sh: line 1: 35877 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/yr/tq_q43k50m795hb4y0njhyth0000gn/T//RtmpsdZi88/file8a3169fd0cf7'
```
NOTE
*** caught segfault ***
address 0x6c69662068637573, cause 'invalid permissions'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
...
6: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
7: suppressMessages(loadNamespace(p))
8: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
9: suppressWarnings(suppressMessages(loadNamespace(p)))
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))), error = function(e) e)
14: tools:::.check_packages_used(package = "fwatlasbc")
An irrecoverable exception occurred. R is aborting now ...
```
## Newly fixed
* checking dependencies in R code ...sh: line 1: 35876 Segmentation fault: 11 R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo 2>&1 < '/var/folders/yr/tq_q43k50m795hb4y0njhyth0000gn/T//RtmpxbUN9R/file8a0e692feb49'
```
NOTE
*** caught segfault ***
address 0x6c69662068637573, cause 'invalid permissions'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package)
...
6: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage"))
7: suppressMessages(loadNamespace(p))
8: withCallingHandlers(expr, warning = function(w) if (inherits(w, classes)) tryInvokeRestart("muffleWarning"))
9: suppressWarnings(suppressMessages(loadNamespace(p)))
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))), error = function(e) e)
14: tools:::.check_packages_used(package = "fwatlasbc")
An irrecoverable exception occurred. R is aborting now ...
```
## In both
* checking examples ... ERROR
```
Running examples in ‘fwatlasbc-Ex.R’ failed
The error most likely occurred in:
> ### Name: fwa_snap_rm_to_point
> ### Title: Snap River Meter to Point
> ### Aliases: fwa_snap_rm_to_point
>
> ### ** Examples
>
> rm <- fwa_add_rms_to_blk(data.frame(blk = 356308001))
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/aylapearson/Code/poissonconsulting/tidyplus/revdep/library.noindex/fwatlasbc/sf/libs/sf.so':
dlopen(/Users/aylapearson/Code/poissonconsulting/tidyplus/revdep/library.noindex/fwatlasbc/sf/libs/sf.so, 0x0006): Library not loaded: /opt/homebrew/opt/gdal/lib/libgdal.35.dylib
Referenced from: <B3C52CEF-2342-3A59-91CF-87D7351AE823> /Users/aylapearson/Code/poissonconsulting/tidyplus/revdep/library.noindex/fwatlasbc/sf/libs/sf.so
Reason: tried: '/opt/homebrew/opt/gdal/lib/libgdal.35.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/homebrew/opt/gdal/lib/libgdal.35.dylib' (no such file), '/opt/homebrew/opt/gdal/lib/libgdal.35.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libgdal.35.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk-11.0.18+10/Contents/Home/lib/server/libgdal.35.dylib' (no such file), '/opt/homebrew/Cellar/gdal/3.10.1/lib/libgdal.35.dylib' (no such file), '/System/Volumes/Preboo
Calls: fwa_add_rms_to_blk ... <Anonymous> -> loadNamespace -> library.dynam -> dyn.load
Execution halted
```
* checking tests ...
```
Running ‘testthat.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 36511 Segmentation fault: 11 ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
27: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
28: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
29: source_file(path, env = env(env), desc = desc, error_call = error_call)
30: FUN(X[[i]], ...)
31: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
...
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
36: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call))
37: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call)
38: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel)
39: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
40: test_check("fwatlasbc")
An irrecoverable exception occurred. R is aborting now ...
```
* checking data for non-ASCII characters ... NOTE
```
Note: found 15 marked UTF-8 strings
```

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