Archives not created `run_eggla_lmm()` about eggla HOT 14 CLOSED

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function call:

res <- run_eggla_lmm(
  data = fread(phenotypes_nopub.csv),
  id_variable = "ID",
  age_days_variable = "days",
  age_years_variable = "age",
  weight_kilograms_variable = "weight",
  height_centimetres_variable = "height",
  sex_variable = "sex",
  covariates = "sourceb",
  male_coded_zero = FALSE,
  random_complexity = 2,
  use_car1 = FALSE,
  parallel = TRUE,
  parallel_n_chunks = 5,
  working_directory = output_directory
)

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Are the two archives still in the folder output_directory?

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Yes the directories remain, they are just empty.

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I meant the zip files?
The zip archives are created at the root of output_directory (in your case) using two sub-directories "male" and "female".
Only the zip archives are kept, while the two directories are deleted.
I can add an option to keep the directories with the outputs in addition to the archives (which contain the same thing).

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Sorry! no they are not, actually they don't appear to be created.

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So, you don't have zip archives.
If yes, then this is the real issue here.

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@burrowsk I changed the way the archives were made.
Could you check if:

1. You had the issue also with the example (code below).

   # pak::pkg_install("mcanouil/eggla@main")
   remotes::install_github("mcanouil/eggla@main")
   
   library(eggla)
   library(data.table)
   data("bmigrowth")
   fwrite(
     x = bmigrowth,
     file = file.path(tempdir(), "bmigrowth.csv")
   )
   res <- run_eggla_lmm(
     data = fread(file.path(tempdir(), "bmigrowth.csv")),
     id_variable = "ID",
     age_days_variable = NULL,
     age_years_variable = "age",
     weight_kilograms_variable = "weight",
     height_centimetres_variable = "height",
     sex_variable = "sex",
     covariates = NULL,
     random_complexity = 1,
     working_directory = tempdir()
   )

2. You do not have the issue anymore with the code below (restart R before).

   # pak::pkg_install("mcanouil/eggla@mcanouil/issue41")
   remotes::install_github("mcanouil/eggla@mcanouil/issue41")
   
   library(eggla)
   library(data.table)
   data("bmigrowth")
   fwrite(
     x = bmigrowth,
     file = file.path(tempdir(), "bmigrowth.csv")
   )
   res <- run_eggla_lmm(
     data = fread(file.path(tempdir(), "bmigrowth.csv")),
     id_variable = "ID",
     age_days_variable = NULL,
     age_years_variable = "age",
     weight_kilograms_variable = "weight",
     height_centimetres_variable = "height",
     sex_variable = "sex",
     covariates = NULL,
     random_complexity = 1,
     working_directory = tempdir()
   )

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With action 1:

• Message upon completion of function about where the archive files are stored
  -- A temp directory is created in my [path]/AppData/Local/Temp/[Rtmp[xxxx]]
• The male and female directories are created here.
• The files are removed from these directories upon completion of the function.
• There are no zip archives
• .rds objects are present

With action 2:

• No message upon completion of function about where the archive files are stored (though can find this myself anyway in AppData/)
• The male and female directories are created in the Rtmp[xxxx] directory
• The male and female directories contain the relevant files
• There are no zip archives created
• . rds objects are present

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For safety/time, my changes included:

• Messages now appeared only if the archives were not created.
• Directories are not deleted if the archives do not exist.

Can you try a more simple example to identify why the archive is not created? I suspect it won't work for you for some reason.

dir.create(file.path(tempdir(), "test_archive"))
cat("text", file = file.path(tempdir(), "test_archive", "test.txt"))
utils::zip(
  zipfile = file.path(tempdir(), "test.zip"),
  files = list.files(file.path(tempdir(), "test_archive"), full.names = TRUE),
  flags = "-r9Xj"
)
#> updating: test.txt (stored 0%)
list.files(tempdir(), "\\.zip$")
#> [1] "test.zip"

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You are right it did not work!
However, looking online it appears it may be due to Rtools. I put Rtools in my path as per https://cran.r-project.org/bin/windows/Rtools/rtools40.html
and now it works. I have just tested both actions from earlier and now I have the archives saved to my Rtmp directory. I've unzipped these and the relevant files are present.

Thanks very much for your help, Windows OS can be so awkward!

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This is what I was thinking about.
To avoid any issues I made some additional changes (5dc0af6) which will allow eggla to work on Windows even without Rtools.
The users will have to archive the results themselves, without the model object.

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Yes, I think that is the best approach. It will be easier for other cohort analysts to archive the results themselves than to mess around with Rtools.

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I am merging #42

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