Error during import

[frenkiboy]

Dear Konrad,

I'm currently trying to switch completely to modules, however I've encountered a quite cryptic error.

When I try to do the following:
helper = modules::import('Functions_Helper')

I get the following error:
no applicable method for 'roclet_tags' applied to an object of class "c('roclet_export', 'roclet')"

I think it might have to do something with the fact that roxygen2 has an import function, which then causes the collision.
R is run with vanilla so there's nothing attached except the standard base stuff.

Here is my session info:

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.4.0 R6_2.2.2       magrittr_1.5   tools_3.4.0    roxygen2_6.0.1
 [6] Rcpp_0.12.11   xml2_1.1.1     stringi_1.1.5  stringr_1.2.0  commonmark_1.2
[11] modules_0.9.7

Any help would be appreciated,

Best,

Vedran

[klmr]

I can’t reproduce the bug but I have an idea what might be causing it. I’ll get back to you soon …!

---

EDIT

master is using the hotfix for now, so just doing devtools::install_github('klmr/modules') will work. The following description is unnecessary.

---

For now, you can probably disable the bug by using the following hotfix branch instead of develop/master: https://github.com/klmr/modules/tree/hotfix-117

To use it, you’ll need to pull this branch and then compile the documentation via

make doc

After that, you can install via devtools::install('.') inside the same directory.

[AkhilGNair]

Hi @klmr

I'm still seeing this with the master branch. A Dockerfile for an env reproducing the behavior is below:

FROM rocker/tidyverse

RUN R -e 'devtools::install_github("klmr/modules@master")' && \
    mkdir pkg && \
    cd pkg && \
    printf 'cat("Hello\n")' > help.r

Building the image as modules and running with

docker run --rm -it modules R

Then executing

modules::import("pkg/help")

Gives the error

Hello
Error in UseMethod("roclet_tags") : 
  no applicable method for 'roclet_tags' applied to an object of class "c('roclet_export', 'roclet')"

Tbh I'm expecting this to be user error, as I managed to use modules before in this manner, but I believe you've changed how things are supposed to be call since I last used it. Could you offer any advice on what's going wrong?

Thanks,
Akhil

PS - Thanks for the excellent package!

[klmr]

This issue shows me that I still haven’t fully grokked how R looks up definitions of S3 objects in different namespaces.

I know what the error is and I can produce a hotfix to work around it. But I’m still trying to figure out how to avoid it properly.

[AkhilGNair]

R is one seriously slippery fish. Is this hotfix hosted? Not that I'm under any illusion that I could help, I'm just interested to see what's causing the error.

[klmr]

Uhm. Never mind — I think?!

Turns out, when re-deploying the existing code without changes everything works. Apparently I had failed to re-generate the NAMESPACE file previously. The following change is all that’s needed:

diff --git a/NAMESPACE b/NAMESPACE
index 443ea2d..88bedd5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,10 +17,6 @@ export(module_help)
 export(module_name)
 export(register_S3_method)
 export(reload)
-export(roclet_clean.roclet_export)
-export(roclet_output.roclet_export)
-export(roclet_process.roclet_export)
-export(roclet_tags.roclet_export)
+S3method(roclet_clean,roclet_export)
+S3method(roclet_output,roclet_export)
+S3method(roclet_process,roclet_export)
+S3method(roclet_tags,roclet_export)
 export(set_script_path)
 export(unload)
 importFrom(roxygen2,roclet_clean)

Anyway, my understanding of S3 lookup in R has been vindicated (again: I think). I’ll fix master ASAP.

[grst]

This issue is back for me (latest version of modules, R 3.6.1).

The bad news is, it only happens in Rstudio (using exactly the same environment as on the command line). Any ideas?

I'm struggling to provide more information as I cannot even reproduce it on the command line (as I said, using the same R installation...). But let me know if you need any additional information.

[mschubert]

Same issue for me on the R command line:

Error in UseMethod("roclet_tags") :
  no applicable method for 'roclet_tags' applied to an
  object of class "c('roclet_rd', 'roclet')"

R 3.6.1, modules 0.9.11, roxygen2 7.0.1 (CRAN) or 7.0.0.9000 (r-lib/roxygen2).

Works with 6.0.1.9000 (klmr/roxygen)

[klmr]

@mschubert To confirm, this is caused by updated roxygen2? Annoying. That said, please open a new issue, this would be unrelated, even if the error message is quite similar.

[klmr]

@grst From Michael’s description I’m guessing you have a different library and thus different version of roxygen2 active in the console and RStudio, can you confirm this?

[grst]

@grst From Michael’s description I’m guessing you have a different library and thus different version of roxygen2 active in the console and RStudio, can you confirm this?

Nope - it's roxygen2 7.0.1 in both cases (both Rstudio and the command line are using the same conda env).

Actually, using the R console it fails, too:

> R
>>> modules::import('test_module')
Error in UseMethod("roclet_tags") : 
  no applicable method for 'roclet_tags' applied to an object of class "c('roclet_rd', 'roclet')"

But using Rscript -e "modules::import('test_module')" works.

[klmr]

OK, thanks for verifying. The reason Rscript -e works is that in non-interactive usage, modules doesn’t parse documentation. Anyway, this is a new issue is because roxygen2 broke backwards compatibility with their new release. The short-term fix is to downgrade roxygen2. I’ll deploy a proper fix once I find time but unfortunately this isn’t trivial since I have no idea how to use the new roxygen2 API, and it isn’t documented.

[klmr]

@grst @mschubert This should now hopefully be fixed (unless I messed up the deployment again). Apologies for the delay.