Required options resulting in error

[zkamvar]

I found some strange behavior where required options results in an error:

'usage: my_program.R [-a -r -m <msg>] <file>

options:
 -a         Add
 -r         Remote
 -m <msg>   Message' -> doc

docopt(doc)

## Error: 
##  usage: my_program.R [-a -r -m <msg>] <file>

It's fixed if you place it as an optional argument:

'usage: my_program.R [-a -r -m <msg>] [<file>]

options:
 -a         Add
 -r         Remote
 -m <msg>   Message' -> doc

docopt(doc)

## List of 8
##  $ -a    : logi FALSE
##  $ -r    : logi FALSE
##  $ -m    : NULL
##  $ <file>: NULL
##  $ a     : logi FALSE
##  $ r     : logi FALSE
##  $ m     : NULL
##  $ file  : NULL
## NULL

Here's the most MWE:

'usage: my_program.R <file>' -> doc
docopt(doc)
## Error: 
##  usage: my_program.R <file>

Session Information:

> devtools::session_info()
Session info -------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, darwin13.4.0        
 ui       RStudio (1.0.8)             
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2016-09-09                  

Packages -----------------------------------------------------------------------------------------
 package  * version date       source        
 devtools   1.12.0  2016-06-24 CRAN (R 3.3.0)
 digest     0.6.10  2016-08-02 CRAN (R 3.3.0)
 docopt   * 0.4.5   2016-06-13 CRAN (R 3.3.0)
 magrittr   1.5     2014-11-22 CRAN (R 3.2.0)
 memoise    1.0.0   2016-01-29 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)
 withr      1.0.2   2016-06-20 cran (@1.0.2) 

[edwindj]

Thx for reporting! I will look into at the end of this week

Best,

Edwin

[dbarowy]

Seconded; please fix this bug. The MWE that @zkamvar produced above was almost exactly my first stab at using docopt.R, which made me think that I was doing something wrong. Glad I thought to check the issue tracker.

[rmwthorne]

+1, I would love to have this working in my scripts

[zkamvar]

Bump.

[edwindj]

Thx for reminding: will look into this before weekend

[zkamvar]

bump

[martabe]

Hi everybody! Just run into the same issue here, when taking the first steps with Docopt. Any fix yet?

[rmwthorne]

@martabe I only had this issue when trying to run in rstudio - if I call my script from the command line, it seems to work

[zkamvar]

FWIW, I got the error running on a cluster. I don't think RStudio has anything to do with it. @rmwthorne, what version are you using?

library("docopt")
'usage: my_program.R [-a -r -m <msg>] <file>

options:
-a         Add
-r         Remote
-m <msg>   Message' -> doc

docopt(doc)
#> Error:
#>  usage: my_program.R [-a -r -m <msg>] <file>

Session info

``` r devtools::session_info() #> Session info ------------------------------------------------------------- #> setting value #> version R version 3.4.3 (2017-11-30) #> system x86_64, darwin15.6.0 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> tz America/Chicago #> date 2018-02-20 #> Packages ----------------------------------------------------------------- #> package * version date source #> backports 1.1.2 2017-12-13 CRAN (R 3.4.3) #> base * 3.4.3 2017-12-07 local #> compiler 3.4.3 2017-12-07 local #> datasets * 3.4.3 2017-12-07 local #> devtools 1.13.4 2017-11-09 CRAN (R 3.4.2) #> digest 0.6.15 2018-01-28 cran (@0.6.15) #> docopt * 0.4.5 2016-06-13 CRAN (R 3.4.0) #> evaluate 0.10.1 2017-06-24 CRAN (R 3.4.1) #> formatR 1.5 2017-04-25 CRAN (R 3.4.0) #> graphics * 3.4.3 2017-12-07 local #> grDevices * 3.4.3 2017-12-07 local #> htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0) #> knitr 1.19 2018-01-29 CRAN (R 3.4.3) #> magrittr 1.5 2014-11-22 CRAN (R 3.4.0) #> memoise 1.1.0 2017-04-21 CRAN (R 3.4.0) #> methods * 3.4.3 2017-12-07 local #> Rcpp 0.12.15 2018-01-20 cran (@0.12.15) #> rmarkdown 1.8 2017-11-17 cran (@1.8) #> rprojroot 1.3-2 2018-01-03 CRAN (R 3.4.3) #> stats * 3.4.3 2017-12-07 local #> stringi 1.1.6 2017-11-17 CRAN (R 3.4.2) #> stringr 1.2.0 2017-02-18 CRAN (R 3.4.0) #> tools 3.4.3 2017-12-07 local #> utils * 3.4.3 2017-12-07 local #> withr 2.1.1.9000 2018-01-09 Github (jimhester/withr@df18523) #> yaml 2.1.16 2017-12-12 CRAN (R 3.4.3) ```

[julian-urbano]

Sorry to intrude, but isn't this behavior correct? In the example, we have an argument <file> which is mandatory, so should always be provided.

When doing docopt(doc) with no arguments, it looks at commandArgs(TRUE), and hence gives the error because there is no <file> argument provided. If we do docopt(doc, "foo") we get the right info:

List of 8
 $ -a    : logi FALSE
 $ -r    : logi FALSE
 $ -m    : NULL
 $ <file>: chr "foo"
 $ a     : logi FALSE
 $ r     : logi FALSE
 $ m     : NULL
 $ file  : chr "foo"
NULL

So the point is that docopt receives both the definition and the actual arguments received. The error you get is not in the definition of the arguments, but in the values received (which are none).

[martabe]

@rmwthorne

I only had this issue when trying to run in rstudio

I see the same behaviour in Rstudio and running the script in the terminal edit: at least with my script. I cannot replicate the same behaviour with the very simple script from @zkamvar: 'usage: my_program.R <file>' -> doc docopt(doc)

I finally ended up using optparse...

Session Information:

> devtools::session_info()
Session info -----------------------------------------------------------------------
 setting  value                       
 version  R version 3.4.3 (2017-11-30)
 system   x86_64, linux-gnu           
 ui       RStudio (1.1.423)           
 language en_US:en                    
 collate  en_US.UTF-8                 
 tz       Europe/Zurich               
 date     2018-02-20                  

Packages --------------------------------------------------------------------------
 package    * version date       source        
 base       * 3.4.3   2017-11-30 local         
 colorspace   1.3-2   2016-12-14 CRAN (R 3.4.3)
 compiler     3.4.3   2017-11-30 local         
 datasets   * 3.4.3   2017-11-30 local         
 devtools     1.13.5  2018-02-18 CRAN (R 3.4.3)
 digest       0.6.15  2018-01-28 CRAN (R 3.4.3)
 docopt     * 0.4.5   2016-06-13 CRAN (R 3.4.3)
 getopt       1.20.2  2018-02-16 CRAN (R 3.4.3)
 ggplot2    * 2.2.1   2016-12-30 CRAN (R 3.4.3)
 graphics   * 3.4.3   2017-11-30 local         
 grDevices  * 3.4.3   2017-11-30 local         
 grid         3.4.3   2017-11-30 local         
 gtable       0.2.0   2016-02-26 CRAN (R 3.4.3)
 labeling     0.3     2014-08-23 CRAN (R 3.4.3)
 lazyeval     0.2.1   2017-10-29 CRAN (R 3.4.3)
 magrittr     1.5     2014-11-22 CRAN (R 3.4.3)
 memoise      1.1.0   2017-04-21 CRAN (R 3.4.3)
 methods    * 3.4.3   2017-11-30 local         
 munsell      0.4.3   2016-02-13 CRAN (R 3.4.3)
 optparse   * 1.4.4   2017-07-18 CRAN (R 3.4.3)
 pillar       1.1.0   2018-01-14 CRAN (R 3.4.3)
 plyr         1.8.4   2016-06-08 CRAN (R 3.4.3)
 Rcpp         0.12.15 2018-01-20 CRAN (R 3.4.3)
 rlang        0.1.6   2017-12-21 CRAN (R 3.4.3)
 rstudioapi   0.7     2017-09-07 CRAN (R 3.4.3)
 scales       0.5.0   2017-08-24 CRAN (R 3.4.3)
 stats      * 3.4.3   2017-11-30 local         
 stringi      1.1.6   2017-11-17 CRAN (R 3.4.3)
 stringr      1.2.0   2017-02-18 CRAN (R 3.4.3)
 tibble       1.4.2   2018-01-22 CRAN (R 3.4.3)
 tools        3.4.3   2017-11-30 local         
 utils      * 3.4.3   2017-11-30 local         
 withr        2.1.1   2017-12-19 CRAN (R 3.4.3)

[zkamvar]

@julian-urbano

Good point! I honestly cannot remember why I thought this was an error and I honestly don't know what I was expecting. I was working at a fever-pitch on finishing my dissertation, so I may not have been thinking clearly.

I thought maybe that it was a behavior only seen when run from Rscript, but when I ran this script:

#!/usr/bin/env Rscript
suppressPackageStartupMessages(library("docopt"))
'usage: my_program.R [-a -r -m <msg>] <file>

options:
 -a         Add
 -r         Remote
 -m <msg>   Message' -> doc

x <- docopt(doc)
print(x)

I get a sensible result.

$ Rscript test.R file.txt
List of 7
 $ -a   : logi FALSE
 $ -r   : logi FALSE
 $ -m   : NULL
 $ file : chr "file.txt"
 $ a    : logi FALSE
 $ r    : logi FALSE
 $ m    : NULL
NULL

The only thing I can think of is that I may have been expecting the full help message to show up, but 🤷‍♂️

All in all, I guess this was a PBKC-type error.

[zkamvar]

I remember now what I was expecting!

The full help message does not print if the input is not correctly specified:

'usage: my_program.R [-a -r -m <msg>] <file>

options:
 -a         Add
 -r         Remote
 -m <msg>   Message' -> doc

docopt(doc)

## Error: 
##  usage: my_program.R [-a -r -m <msg>] <file>

One would expect the error message to be:

usage: my_program.R [-a -r -m <msg>] <file>

options:
 -a         Add
 -r         Remote
 -m <msg>   Message

[edwindj]

Agreed and good one! However in conflict with staying close to the docopt.py implementation (have to check that)