packrat::status() fails with Rmd files

[aschmu]

Hi,
I have a fairly complex projet that uses packrat and it's recently been failing with usual packrat function calls such as a status() or clean().
Here 's the output :

> packrat::unused_packages()
Error in eval(expr, envir, enclos) : objet 'html_output' introuvable

and my R session in the packrat managed top directory.

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 24 (Twenty Four)

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

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

other attached packages:
[1] packrat_0.4.8-54  wranglr_0.1.0     data.table_1.10.4 sqltools_0.1.1   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12     rstudioapi_0.6   bindr_0.1        knitr_1.15.1    
 [5] magrittr_1.5     R6_2.2.2         rlang_0.1.2      httr_1.2.1      
 [9] stringr_1.2.0    dplyr_0.7.3      tools_3.3.2      withr_1.0.2     
[13] htmltools_0.3.6  yaml_2.1.14      assertthat_0.2.0 digest_0.6.12   
[17] rprojroot_1.2    tibble_1.3.4     bindrcpp_0.2     infuser_0.2.6   
[21] RODBC_1.3-14     curl_2.8.1       memoise_1.0.0    glue_1.1.1      
[25] evaluate_0.10    rmarkdown_1.8    stringi_1.1.5    backports_1.0.5 
[29] pkgconfig_2.0.1 
> 

[kevinushey]

Can you try running again with options(error = traceback) so I can see what code is executing? E.g.

options(error = traceback)
packrat::unused_packages()

[aschmu]

Here's what I'm getting. Not super useful (objet 'html_output' introuvable means *** could not be found).

> options(error=traceback)
> packrat::unused_packages()
Error in eval(expr, envir, enclos) : objet 'html_output' introuvable
2: print.session_info(x)
1: function (x, ...) 
   UseMethod("print")(x)

[aschmu]

Any idea what might be causing this ?
For now I'm having to manually move all Rmd files before packrat operations and then putting them back where they were once I'm done (e.g mv *.Rmd ../backup/-> packat::status() -> packat::snapshot() - > mv ../backup/*.Rmd .).
But this is clearly a tedious process.

[kevinushey]

I don't have a good idea :-/ The error would imply that you're using a variable called html_output somewhere, but I'm not sure what package would be providing it or looking for it.

There should be a way of finding out what R code is being executed with some combination of

options(error = recover)
options(error = traceback)

but unfortunately the traceback I saw in your recent post didn't provide too much information (that seems to imply that the attempt to print session info was causing an error?)

[aronatkins]

This problem was caused by using rmarkdown::render to analyze R Markdown files for dependencies.

We believe that this is resolved with #647.