use_spell_check() does not find typos

[JBGruber]

First of all: Thanks for this awsome package. It made developing packages so incredibly easy!

Now the issue I have: I used usethis::use_spell_check() to add an automatic spell check to a little fun package I wrote: www.github.com/JBGruber/rwhatsapp

Now I found a typo in the documentation which was not picked up before. The typo is reported by spelling::spell_check_package() though. Not sure if I understand something wrong but I though usethis::use_spell_check() would cause a warning when running devtools::check().

reprex

I use the said package as reprex. You could also try it by adding a typo to one of your own.

system("git clone https://github.com/JBGruber/rwhatsapp.git")
setwd("./rwhatsapp")
lines <- readLines("./R/rwhatsapp.R")
lines[grepl("#'   problems you can provide a", lines)] <- gsub(
  x = lines[grepl("#'   problems you can provide a", lines)],
  pattern = "custom",
  replacement = "cudtom"
)
writeLines(lines, "./R/rwhatsapp.R")
roxygen2::roxygenise(clean = TRUE)
devtools::check()
spelling::spell_check_package()
session_info()

some output

These are the last lines of output for me when running devtools::check() and the output of spelling::spell_check_package()

✔  Running ‘spelling.R’
✔  Running ‘testthat.R’
   
   
── R CMD check results ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────── rwhatsapp 0.1.3.9000 ────
Duration: 28.7s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔
> spelling::spell_check_package()
  WORD     FOUND IN
cudtom   rwa_read.Rd:18

And here comes my session_info() in case you need it.

> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 os       Ubuntu 18.04.1 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language en_GB:en                    
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       Europe/London               
 date     2018-12-07                  

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 !  package     * version    date       lib source                            
    assertthat    0.2.0      2017-04-11 [1] CRAN (R 3.5.0)                    
    backports     1.1.2      2017-12-13 [1] CRAN (R 3.5.0)                    
    base64enc     0.1-3      2015-07-28 [1] CRAN (R 3.5.0)                    
    bindr         0.1.1      2018-03-13 [1] CRAN (R 3.5.0)                    
    bindrcpp      0.2.2      2018-03-29 [1] CRAN (R 3.5.0)                    
    broom         0.5.1      2018-12-05 [1] CRAN (R 3.5.1)                    
    callr         3.0.0      2018-08-24 [1] CRAN (R 3.5.1)                    
    cli           1.0.1      2018-09-25 [1] CRAN (R 3.5.1)                    
    commonmark    1.7        2018-12-01 [1] CRAN (R 3.5.1)                    
    covr          3.2.1      2018-10-18 [1] CRAN (R 3.5.1)                    
    crayon        1.3.4      2017-09-16 [1] CRAN (R 3.5.0)                    
    desc          1.2.0      2018-05-01 [1] CRAN (R 3.5.0)                    
    devtools    * 2.0.1      2018-10-26 [1] CRAN (R 3.5.1)                    
    digest        0.6.18     2018-10-10 [1] CRAN (R 3.5.1)                    
    dplyr         0.7.8      2018-11-10 [1] CRAN (R 3.5.1)                    
    fs            1.2.6      2018-08-23 [1] CRAN (R 3.5.1)                    
    generics      0.0.2      2018-11-29 [1] CRAN (R 3.5.1)                    
    glue          1.3.0      2018-11-09 [1] Github (tidyverse/glue@35c61e9)   
    hunspell      2.9        2017-12-16 [1] CRAN (R 3.5.0)                    
    janeaustenr   0.1.5      2017-06-10 [1] CRAN (R 3.5.1)                    
    lattice       0.20-38    2018-11-04 [4] CRAN (R 3.5.1)                    
    lazyeval      0.2.1      2017-10-29 [1] CRAN (R 3.5.0)                    
    magrittr      1.5        2014-11-22 [1] CRAN (R 3.5.0)                    
    Matrix        1.2-15     2018-11-01 [4] CRAN (R 3.5.1)                    
    memoise       1.1.0      2017-04-21 [1] CRAN (R 3.5.0)                    
    nlme          3.1-137    2018-04-07 [4] CRAN (R 3.5.0)                    
    pillar        1.3.0      2018-07-14 [1] CRAN (R 3.5.1)                    
    pkgbuild      1.0.2      2018-10-16 [1] CRAN (R 3.5.1)                    
    pkgconfig     2.0.2      2018-08-16 [1] CRAN (R 3.5.1)                    
    pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.5.1)                    
    prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.5.0)                    
    processx      3.2.1      2018-12-05 [1] CRAN (R 3.5.1)                    
    ps            1.2.1      2018-11-06 [1] CRAN (R 3.5.1)                    
    purrr         0.2.5      2018-05-29 [1] CRAN (R 3.5.0)                    
    R6            2.3.0      2018-10-04 [1] CRAN (R 3.5.1)                    
    rcmdcheck     1.3.2      2018-11-10 [1] CRAN (R 3.5.1)                    
    Rcpp          1.0.0      2018-11-07 [1] CRAN (R 3.5.1)                    
    remotes       2.0.2      2018-10-30 [1] CRAN (R 3.5.1)                    
    rex           1.1.2      2017-10-19 [1] CRAN (R 3.5.0)                    
    rlang         0.3.0.1    2018-10-25 [1] CRAN (R 3.5.1)                    
    roxygen2    * 6.1.1      2018-11-07 [1] CRAN (R 3.5.1)                    
    rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.5.0)                    
    rstudioapi    0.8        2018-10-02 [1] CRAN (R 3.5.1)                    
 VP rwhatsapp   * 0.1.3.9000 2018-12-07 [?] local                             
    sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.5.1)                    
    SnowballC     0.5.1      2014-08-09 [1] CRAN (R 3.5.0)                    
    spelling      1.2        2018-12-07 [1] Github (ropensci/spelling@5c6d160)
    stringi       1.2.4      2018-07-20 [1] CRAN (R 3.5.1)                    
    stringr       1.3.1      2018-05-10 [1] CRAN (R 3.5.0)                    
    testthat      2.0.1      2018-10-13 [1] CRAN (R 3.5.1)                    
    tibble        1.4.2      2018-01-22 [1] CRAN (R 3.5.0)                    
    tidyr         0.8.2      2018-10-28 [1] CRAN (R 3.5.1)                    
    tidyselect    0.2.5      2018-10-11 [1] CRAN (R 3.5.1)                    
    tidytext      0.2.0      2018-10-17 [1] CRAN (R 3.5.1)                    
    tokenizers    0.2.1      2018-03-29 [1] CRAN (R 3.5.1)                    
    usethis     * 1.4.0      2018-08-14 [1] CRAN (R 3.5.1)                    
    withr         2.1.2      2018-03-15 [1] CRAN (R 3.5.0)                    
    xml2          1.2.0      2018-01-24 [1] CRAN (R 3.5.0)                    
    xopen         1.0.0      2018-09-17 [1] CRAN (R 3.5.1)                    
    yaml          2.2.0      2018-07-25 [1] CRAN (R 3.5.1)      

Thanks!

[JBGruber]

I did some digging and found this in the documentation for spelling::spell_check_setup (which I realised is used under the hood here):

"The spell_check_setup function adds a unit test to your package which automatically runs a spellcheck on documentation and vignettes during R CMD check if the environment variableNOT_CRANis set to TRUE. "

For me, this variable was not set. After setting Sys.setenv(NOT_CRAN = TRUE), all works as intended.

I then used usethis::edit_r_environ("project") to add this to my package's project. Maybe this could be included either as a suggestion or it could be done automatically?

Or I could create a new issue in the spelling package since it seems to me like this should be included in spelling::spell_check_setup anyway or at least made more explicit in the documentation.

[jennybc]

I think the devtools-verse does generally set NOT_CRAN = TRUE (yes @jimhester?). I see evidence of this spellcheck test when I use check() locally, but we have a printing problem that makes the output impossible to see, at least in RStudio (r-lib/rcmdcheck#88).

✔  checking for unstated dependencies in ‘tests’ ...
─  checking tests ...
✔< yaml       use_pkgdown.Rd:13 (1.8s)ing.Rout.save’ ...
✔  Running ‘testthat.R’ [10s/11s]

So several things are interacting here. In any case, I don't think there is anything to be done about it in usethis.

I note that the test results show up beautifully for me in travis logs, e.g. https://travis-ci.org/r-lib/usethis/jobs/466364994#L1202-L1219

Until the rcmdcheck issue is fixed, that's where I'm looking.

cc @jeroen @gaborcsardi

[JBGruber]

Thanks @jennybc for looking into this.

I just realised that everything works fine when I use Build -> Check Package in RStudio instead of typing devtools::check().

> checking tests ...
  See below...

-- Test failures ------------------------------------------------- spelling ----

> if(requireNamespace('spelling', quietly=TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = TRUE, skip_on_cran = TRUE)
Error: Potential spelling errors: cudtom
Execution halted

1 error x | 0 warnings v | 0 notes v
Error: R CMD check found ERRORs
Execution halted

Exited with status 1.

I'm still a bit confused why this happens (so it would be great if someone wants to elaborate) but at least I know how to get around it.

About the printing problem: I prefer the tests to fail when there is a misspelled word. So I can either resolve it or add to my WORDLIST. So I didn't even notice that.

Anyway, it seems usethis and spelling are fine!