Updates

[Krgaric]

No description provided.

[leifeld]

See comment. Also, it may make sense to fix the size issue in the same PR. The problem only occurs if every 8 hours or if you restart R.

[leifeld]

Is rlang an object or function exported by ggplot2? I thought it was an independent package. You need to add something like this to every function that uses .data: @importFrom rlang .data. I.e., also to the other autoplot methods that use this. Then recompile the documentation.

[leifeld]

Thanks, please fix as per my comments, then we'll see if it still produces errors (other than the ones I expect).

[leifeld]

Let's try to wrap this PR up soon. Did you want to add anything else regarding aes_string or backbone plotting? Can you make the requested changes? Thanks.

[Krgaric]

All previous comments resolved. There is still an issue with autoplot function in dna_backbone. Here is the error log:

Error in ggplot2::geom_line(): ! Problem while computing aesthetics. ℹ Error occurred in the 1st layer. Caused by error: ! Can't subset .dataoutside of a data mask context. Runrlang::last_trace()` to see where the error occurred.

rlang::last_trace()
<error/rlang_error>
Error in ggplot2::geom_line():
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! Can't subset .data outside of a data mask context.

---

Backtrace:
▆

1. ├─base (local) <fn>(x)
2. ├─ggplot2:::print.ggplot(x)
3. │ ├─ggplot2::ggplot_build(x)
4. │ └─ggplot2:::ggplot_build.ggplot(x)
5. │ └─ggplot2:::by_layer(...)
6. │ ├─rlang::try_fetch(...)
7. │ │ ├─base::tryCatch(...)
8. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
11. │ │ └─base::withCallingHandlers(...)
12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
13. │ └─l$compute_aesthetics(d, plot)
14. │ └─ggplot2 (local) compute_aesthetics(..., self = self)
15. │ └─ggplot2:::scales_add_defaults(...)
16. │ └─base::lapply(aesthetics[new_aesthetics], eval_tidy, data = data)
17. │ └─rlang (local) FUN(X[[i]], ...)
18. ├─rlang::.data[["iteration"]]
19. └─rlang:::[[.rlang_fake_data_pronoun(rlang::.data, "iteration")
20. └─rlang:::stop_fake_data_subset(call)

21. └─rlang::abort(...)
    

The error occurs somewhere between lines 2851 and 2956. I checked all the geom_lines where "iteration" appears but cannot find anything odd.

[leifeld]

Thanks. I hope you can figure it out. Let me tag @TimHenrichsen . Tim, can you help? Kristijan fixed the aes_string problem, but there is some issue with the backbone autoplot code.

[TimHenrichsen]

Hi Kristijan and thanks for all the work! I could reproduce your issue and noticed that I also couldn't compute other autoplot functions. I checked the .data help file which says the following:

The .data pronoun is automatically created for you by data-masking functions using the tidy eval framework. You don't need to import rlang::.data or use library(rlang) to work with this pronoun.

However, the .data object exported from rlang is useful to import in your package namespace to avoid a ⁠R CMD check⁠ note when referring to objects from the data mask. R does not have any way of knowing about the presence or absence of .data in a particular scope so you need to import it explicitly or equivalently declare it with utils::globalVariables(".data").

Note that rlang::.data is a "fake" pronoun. Do not refer to rlang::.data with the ⁠rlang::⁠ qualifier in data masking code. Use the unqualified .data symbol that is automatically put in scope by data-masking functions.

Could you test if the autoplot functions work, when you remove rlang:: before every .data command?

[Krgaric]

Hi Kristijan and thanks for all the work! I could reproduce your issue and noticed that I also couldn't compute other autoplot functions. I checked the .data help file which says the following:

The .data pronoun is automatically created for you by data-masking functions using the tidy eval framework. You don't need to import rlang::.data or use library(rlang) to work with this pronoun.

However, the .data object exported from rlang is useful to import in your package namespace to avoid a ⁠R CMD check⁠ note when referring to objects from the data mask. R does not have any way of knowing about the presence or absence of .data in a particular scope so you need to import it explicitly or equivalently declare it with utils::globalVariables(".data").

Note that rlang::.data is a "fake" pronoun. Do not refer to rlang::.data with the ⁠rlang::⁠ qualifier in data masking code. Use the unqualified .data symbol that is automatically put in scope by data-masking functions.

Could you test if the autoplot functions work, when you remove rlang:: before every .data command?

Dear @TimHenrichsen, thank you, it works now. It plots as supposed, but there are some warning messages that should be checked out:
Warning messages:
1: Removed 499 rows containing missing values (geom_line()).
2: Removed 998 rows containing missing values (geom_line()).
3: Removed 499 rows containing missing values (geom_line()).

use the gridExtra package to arrange the diagnostics in a single plot

library("gridExtra")
grid.arrange(p[[1]], p[[2]], p[[3]], p[[4]])
Don't know how to automatically pick scale for object of type . Defaulting to continuous.
Don't know how to automatically pick scale for object of type . Defaulting to continuous.
Warning messages:
1: Removed 499 rows containing missing values (geom_line()).
2: Removed 998 rows containing missing values (geom_line()).
3: Removed 499 rows containing missing values (geom_line()).

This was ran on the sample example. Is something like that expected?

Thank you for the help so far!

[leifeld]

The checks below say that you need to put rlang in the DESCRIPTION file under Imports.

[Krgaric]

The checks below say that you need to put rlang in the DESCRIPTION file under Imports.

Resolved.

[leifeld]

You forgot the comma in the line before. See new errors in the check log below.