infinite loop of as.vector(x, mode) in default_usage.s4method

[muschellij2]

Cross-posting something from the roxygen package (r-lib/roxygen2#475) from klutometis/roxygen @klutometis. If

Error

When trying to document using devtools::document getting C stack usage error on R 3.3.0:

devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette'))
Updating extrantsr documentation
Loading extrantsr
Error: C stack usage  7970652 is too close to the limit

Traceback

After running traceback() you get as.vector(x, mode) repeated over and over and then the tail is:

29: as.vector(x, mode)
28: as.vector(x, mode)
27: as.vector(x, "character")
26: as.vector(x, "character")
25: as.character.default(x$value@defined)
24: as.character(x$value@defined)
23: format_name(name)
22: eval(expr, envir, enclos)
21: eval(arg, env)
20: escape(eval(arg, env))
19: FUN(X[[i]], ...)
18: lapply(args, function(arg) {
        if (is.character(arg)) 
            return(arg)
        escape(eval(arg, env))
    })
17: build_rd(format_name(name), "(", arglist, ")")
16: function_usage(x$value@generic, formals(x$value), s4method)
15: default_usage.s4method(partitum$object)
14: default_usage(partitum$object)
13: wrap_string(default_usage(partitum$object))
12: process_usage(block)
11: add_tag(rd, process_usage(block))
10: block_to_rd(block, base_path, parsed$env)
9: roc_process.rd_roclet(roc, parsed, base_path, options = options)
8: roc_process(roc, parsed, base_path, options = options)
7: FUN(X[[i]], ...)
6: lapply(roclets, roc_out)
5: unlist(lapply(roclets, roc_out))
4: roxygen2::roxygenise(pkg$path, roclets = roclets, load_code = ns_env)
3: force(code)
2: withr::with_envvar(r_env_vars(), roxygen2::roxygenise(pkg$path, 
       roclets = roclets, load_code = ns_env))
1: devtools::document(roclets = c("rd", "collate", "namespace", 
       "vignette"))

which seems like there may be some change using format_name, but I can't assess yet. I'll keep looking but currently unsure where the breakdown is. If I find, I'll try to make a PR.

Session information

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] extrantsr_1.1.15.0 colorout_1.1-0    

loaded via a namespace (and not attached):
 [1] hash_2.2.6           Rcpp_0.12.5          magrittr_1.5        
 [4] roxygen2_5.0.1.9000  splines_3.3.0        devtools_1.11.1.9000
 [7] munsell_0.4.3        lattice_0.20-33      colorspace_1.2-6    
[10] stringr_1.0.0        plyr_1.8.4           tools_3.3.0         
[13] parallel_3.3.0       grid_3.3.0           yaImpute_1.0-26     
[16] neuroim_0.0.6        nlme_3.1-128         mgcv_1.8-12         
[19] R.oo_1.20.0          oro.nifti_0.5.4      R.matlab_3.5.1      
[22] withr_1.0.2          iterators_1.0.8      matrixStats_0.50.2  
[25] rgl_0.95.1441        assertthat_0.1       abind_1.4-3         
[28] digest_0.6.9         WhiteStripe_1.1.3    Matrix_1.2-6        
[31] readr_0.2.2          R.utils_2.3.0        bitops_1.0-6        
[34] memoise_1.0.0        stringi_1.1.1        ANTsR_0.3.2         
[37] fslr_1.6.5.2         scales_0.4.0         R.methodsS3_1.7.1   
> devtools::session_info()
Session info -------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.0 (2016-05-03)
 system   x86_64, darwin13.4.0        
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2016-06-22                  

Packages -----------------------------------------------------------------------
 package     * version     date       source                             
 abind         1.4-3       2015-03-13 CRAN (R 3.2.0)                     
 ANTsR         0.3.2       2016-05-24 local                              
 assertthat    0.1         2013-12-06 CRAN (R 3.2.0)                     
 bitops        1.0-6       2013-08-17 CRAN (R 3.2.0)                     
 colorout    * 1.1-0       2015-04-20 Github (jalvesaq/colorout@1539f1f) 
 colorspace    1.2-6       2015-03-11 CRAN (R 3.2.0)                     
 devtools      1.11.1.9000 2016-06-22 Github (hadley/devtools@d247c17)   
 digest        0.6.9       2016-01-08 CRAN (R 3.2.3)                     
 extrantsr   * 1.1.15.0    <NA>       local                              
 fslr          1.6.5.2     2016-06-08 local                              
 hash          2.2.6       2013-02-21 CRAN (R 3.2.0)                     
 iterators     1.0.8       2015-10-13 CRAN (R 3.2.0)                     
 lattice       0.20-33     2015-07-14 CRAN (R 3.3.0)                     
 magrittr      1.5         2014-11-22 CRAN (R 3.2.0)                     
 Matrix        1.2-6       2016-05-02 CRAN (R 3.3.0)                     
 matrixStats   0.50.2      2016-04-24 CRAN (R 3.2.5)                     
 memoise       1.0.0       2016-01-29 CRAN (R 3.2.3)                     
 mgcv          1.8-12      2016-03-03 CRAN (R 3.3.0)                     
 munsell       0.4.3       2016-02-13 CRAN (R 3.2.3)                     
 neuroim       0.0.6       2016-01-07 CRAN (R 3.2.3)                     
 nlme          3.1-128     2016-05-10 CRAN (R 3.3.0)                     
 oro.nifti     0.5.4       2016-06-08 Github (bjw34032/oro.nifti@e0af126)
 plyr          1.8.4       2016-06-08 CRAN (R 3.3.0)                     
 R.matlab      3.5.1       2016-03-28 CRAN (R 3.2.4)                     
 R.methodsS3   1.7.1       2016-02-16 CRAN (R 3.2.3)                     
 R.oo          1.20.0      2016-02-17 CRAN (R 3.2.3)                     
 R.utils       2.3.0       2016-04-14 CRAN (R 3.2.5)                     
 Rcpp          0.12.5      2016-05-14 CRAN (R 3.2.5)                     
 readr         0.2.2       2015-10-22 CRAN (R 3.2.0)                     
 rgl           0.95.1441   2016-01-04 CRAN (R 3.2.3)                     
 roxygen2      5.0.1.9000  2016-06-22 Github (klutometis/roxygen@7133fd6)
 scales        0.4.0       2016-02-26 CRAN (R 3.2.3)                     
 stringi       1.1.1       2016-05-27 CRAN (R 3.3.0)                     
 stringr       1.0.0       2015-04-30 CRAN (R 3.2.0)                     
 WhiteStripe   1.1.3       2016-05-31 local                              
 withr         1.0.2       2016-06-20 CRAN (R 3.3.0)                     
 yaImpute      1.0-26      2015-07-20 CRAN (R 3.2.0)                     

[EricArcher]

I can confirm that this error does not occur in R 3.2.4 revised, but does occur in 3.3.0.

The error I get can be replicated with the following object:

> x$value@defined
An object of class “signature”
       x 
"gtypes" 
> str(x$value@defined)
Formal class 'signature' [package "methods"] with 3 slots
  ..@ .Data  : chr "gtypes"
  ..@ names  : chr "x"
  ..@ package: chr "roxygen_devtest"

In R 3.2.4, this is the result I get:

> as.vector(x$value@defined, "character")
[1] "gtypes"

In R 3.3.0, I get the C stack error described above and in [https://github.com/r-lib/roxygen2/issues/475]

In the NEWS file for 3.3.0 there are these two lines that might be relevant:

C-LEVEL FACILITIES:

    * New API call R_orderVector1, a faster one-argument version of
      R_orderVector.


  BUG FIXES:

    * C-level asChar(x) is fixed for when x is not a vector, and it
      returns "TRUE"/"FALSE" instead of "T"/"F" for logical vectors.

[muschellij2]

Thought this was fixed with 3.3.1 - it was not.

[EricArcher]

Based on a suggestion by Luke Tierney, I removed packages one-by-one to see if I could make the error go away with that. When I removed Matrix (v1.2-6 on R 3.3.1), I got no error. Matrix automatically reinstalls (same version), but all is good now.

[hadley]

This seems like a roxygen2 issue, not devtools.

[lock]

This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/