reverse dependency problem with ggalluvial

[corybrunson]

Hi, i'm the maintainer of {ggalluvial} and about to release a new patch to CRAN. Running revdepcheck::revdep_check() identified a problem with (i think) the development version of {projectR}, but i have not been able to parse the problem. I've copied the report below.

Would you be able to check {projectR} after installing the current development version of {ggalluvial}? You can use remotes::install_github("corybrunson/ggalluvial") with no additional arguments.

Thank you! Please let me know if i've missed something.

Report generated by {revdepcheck} and output to 'problems.md':

# projectR

<details>

* Version: 1.14.0
* GitHub: https://github.com/genesofeve/projectR
* Source code: https://github.com/cran/projectR
* Date/Publication: 2022-11-02
* Number of recursive dependencies: 173

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

</details>

## Newly broken

*   checking examples ...sh: line 1: 42932 Illegal instruction: 4  LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'projectR-Ex.Rout' 2>&1 < 'projectR-Ex.R'
    ```
     ERROR
    Running examples in ‘projectR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: projectR
    > ### Title: Generic projectR function
    > ### Aliases: projectR projectR,matrix,matrix-method
    > ###   projectR,matrix,LinearEmbeddingMatrix-method
    > ###   projectR,matrix,prcomp-method projectR,matrix,rotatoR-method
    > ###   projectR,matrix,correlateR-method projectR,matrix,hclust-method
    ...
    maxGibbsMass   100 
    
    
     *** caught illegal operation ***
    address 0x109c8bc9b, cause 'illegal opcode'
    
    Traceback:
     1: dispatchFunc(data, allParams, uncertainty)
     2: CoGAPS(p.RNAseq6l3c3t, params = new("CogapsParams", nPatterns = 5))
    An irrecoverable exception occurred. R is aborting now ...
    ```

## Newly fixed

*   checking examples ...sh: line 1: 42543 Illegal instruction: 4  LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'projectR-Ex.Rout' 2>&1 < 'projectR-Ex.R'
    ```
     ERROR
    Running examples in ‘projectR-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: projectR
    > ### Title: Generic projectR function
    > ### Aliases: projectR projectR,matrix,matrix-method
    > ###   projectR,matrix,LinearEmbeddingMatrix-method
    > ###   projectR,matrix,prcomp-method projectR,matrix,rotatoR-method
    > ###   projectR,matrix,correlateR-method projectR,matrix,hclust-method
    ...
    maxGibbsMass   100 
    
    
     *** caught illegal operation ***
    address 0x10e91fc9b, cause 'illegal opcode'
    
    Traceback:
     1: dispatchFunc(data, allParams, uncertainty)
     2: CoGAPS(p.RNAseq6l3c3t, params = new("CogapsParams", nPatterns = 5))
    An irrecoverable exception occurred. R is aborting now ...
    ```

## In both

*   checking tests ...
    ```
      Running ‘testthat.R’/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 42957 Illegal instruction: 4  ${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:
      24: 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) {    })
      25: test_code(NULL, exprs, env)
      26: source_file(path, child_env(env), wrap = wrap)
      27: FUN(X[[i]], ...)
      28: lapply(test_paths, test_one_file, env = env, wrap = wrap)
    ...
      29: doTryCatch(return(expr), name, parentenv, handler)
      30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
      31: tryCatchList(expr, classes, parentenv, handlers)
      32: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
      33: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, wrap = wrap))
      34: 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,     wrap = wrap, load_package = load_package)
      35: 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,     wrap = wrap, load_package = load_package, parallel = parallel)
      36: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
      37: test_check("projectR")
      An irrecoverable exception occurred. R is aborting now ...
    ```

*   checking for hidden files and directories ... NOTE
    ```
    Found the following hidden files and directories:
      .travis.yml
    These were most likely included in error. See section ‘Package
    structure’ in the ‘Writing R Extensions’ manual.
    ```

*   checking top-level files ... NOTE
    ```
    File
      LICENSE
    is not mentioned in the DESCRIPTION file.
    ```

*   checking R code for possible problems ... NOTE
    ```
    alluvialMat: no visible binding for global variable ‘celltype’
    alluvialMat: no visible binding for global variable ‘variable’
    alluvialMat: no visible binding for global variable ‘value’
    alluvialMat: no visible binding for global variable ‘nCells’
    alluvialMat: no visible binding for global variable ‘nCells_per_type’
    alluvialMat: no visible binding for global variable
      ‘nCells_per_pattern’
    alluvialMat: no visible binding for global variable ‘prop’
    Undefined global functions or variables:
      celltype nCells nCells_per_pattern nCells_per_type prop value
      variable
    ```

*   checking for unstated dependencies in vignettes ... NOTE
    ```
    'library' or 'require' call not declared from: ‘gplots’
    ```

[corybrunson]

Update: I apologize; it did not even occur to me to run the check myself. I installed the development version of {ggalluvial} and cloned this repo in order to run devtools::test() and devtools::check().

I got some warnings from the tests due to updates to {testthat} syntax and the following several NOTEs that might be related to {ggalluvial}:

❯ checking R code for possible problems ... NOTE
  alluvialMat: no visible binding for global variable ‘celltype’
  alluvialMat: no visible binding for global variable ‘variable’
  alluvialMat: no visible binding for global variable ‘value’
  alluvialMat: no visible binding for global variable ‘nCells’
  alluvialMat: no visible binding for global variable ‘nCells_per_type’
  alluvialMat: no visible binding for global variable
    ‘nCells_per_pattern’
  alluvialMat: no visible binding for global variable ‘prop’
  alluvialMat: no visible binding for global variable ‘stratum’
  plotConfidenceIntervals: no visible binding for global variable ‘high’
  plotConfidenceIntervals: no visible binding for global variable ‘low’
  plotConfidenceIntervals: no visible binding for global variable ‘mid’
  plotConfidenceIntervals: no visible binding for global variable ‘idx’
  plotConfidenceIntervals: no visible binding for global variable
    ‘positive’
  Undefined global functions or variables:
    celltype high idx low mid nCells nCells_per_pattern nCells_per_type
    positive prop stratum value variable

Though they don't seem to resolve the serious ERROR above.

[Gaura]

Hi @corybrunson!

Thanks for reporting. Yes, I am also getting this error. However, it doesn't seem to be related to ggalluvial. At first glance, it looks like it has to do with the package CoGAPS but I need to look into it. It occurs even without using the latest ggalluvial version on Github. So, if it doesn't impede your patch, please go ahead. I'll look into this error and resolve it.

Good luck with your package!

[corybrunson]

@Gaura thanks for that! I'll continue with the release.