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roxygen 5.0.0 does not recognize its tags anymore #422

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Starfox899 opened this issue Nov 2, 2015 · 12 comments
Closed

roxygen 5.0.0 does not recognize its tags anymore #422

Starfox899 opened this issue Nov 2, 2015 · 12 comments

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@Starfox899
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@Starfox899 Starfox899 commented Nov 2, 2015

Dear all,

after having upgraded to roxygen2 5.0.0 I am recognizing strange behavior. Inparticular roxygen tells me any tag is unknown. As a result NAMESPACE and others are all empty. Any ideas why this is happening?

Example:

> devtools::document()
Updating rpnfext documentation
Loading rpnfext
Writing NAMESPACE
There were 28 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: @title [foo.R#1]: unknown tag
2: @description [foo.R#1]: unknown tag
3: @export [foo.R#4]: unknown tag
4: @title [foo.R#1]: unknown tag
5: @description [foo.R#1]: unknown tag
6: @export [foo.R#25]: unknown tag
7: @title [foo.R#1]: unknown tag
8: @description [foo.R#1]: unknown tag
9: @export [foo.R#45]: unknown tag
10: @title [getSymbolsForIndexSymbols.R#2]: unknown tag
11: @param [getSymbolsForIndexSymbols.R#4]: unknown tag
12: @param [getSymbolsForIndexSymbols.R#5]: unknown tag
13: @return [getSymbolsForIndexSymbols.R#7]: unknown tag
14: @import [getSymbolsForIndexSymbols.R#8]: unknown tag
15: @import [getSymbolsForIndexSymbols.R#9]: unknown tag
16: @export [getSymbolsForIndexSymbols.R#10]: unknown tag
17: @title [processor-wrappers.R#1]: unknown tag
18: @description [processor-wrappers.R#1]: unknown tag
19: @param [processor-wrappers.R#8]: unknown tag
20: @param [processor-wrappers.R#9]: unknown tag
21: @param [processor-wrappers.R#10]: unknown tag
22: @inheritParams [processor-wrappers.R#11]: unknown tag
23: @return [processor-wrappers.R#12]: unknown tag
24: @export [processor-wrappers.R#13]: unknown tag
25: @seealso [processor-wrappers.R#14]: unknown tag
26: @references [processor-wrappers.R#15]: unknown tag
27: @import [processor-wrappers.R#16]: unknown tag
28: @examples [processor-wrappers.R#17]: unknown tag
@emhart
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@emhart emhart commented Nov 2, 2015

I'm having a similar issue see this gist for session info. I created a test directory that had the single fxn str_length() pulled from the read me and created a dummy package directory structure. Everything works fine with 4.1.1 when I install the OSX binary on CRAN but when I instally v. 5.0.0 from source I get the same error as above and on my gist.

@hadley
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@hadley hadley commented Nov 2, 2015

Could you please both provide devtools::session_info() and ls(roxygen2:::tags)? I'm not sure what's different on your systems compared to everyone else.

@emhart
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@emhart emhart commented Nov 2, 2015

>  devtools::session_info()
Session info ------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.1.3 (2015-03-09)
 system   x86_64, darwin13.4.0        
 ui       RStudio (0.99.667)          
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Los_Angeles         

> Packages ----------------------------------------------------------------------------------------
 package    * version date       source        
 colorspace * 1.2-6   2015-03-11 CRAN (R 3.1.3)
 devtools     1.7.0   2015-01-17 CRAN (R 3.1.2)
 digest     * 0.6.8   2014-12-31 CRAN (R 3.1.2)
 ggplot2      1.0.1   2015-03-17 CRAN (R 3.1.3)
 gtable     * 0.1.2   2012-12-05 CRAN (R 3.1.0)
 httr         1.0.0   2015-06-25 CRAN (R 3.1.3)
 lattice    * 0.20-31 2015-03-30 CRAN (R 3.1.3)
 magrittr   * 1.5     2014-11-22 CRAN (R 3.1.2)
 MASS       * 7.3-40  2015-03-21 CRAN (R 3.1.3)
 memoise    * 0.2.1   2014-04-22 CRAN (R 3.1.0)
 munsell    * 0.4.2   2013-07-11 CRAN (R 3.1.0)
 plyr       * 1.8.2   2015-04-21 CRAN (R 3.1.3)
 proto      * 0.3-10  2012-12-22 CRAN (R 3.1.0)
 R6         * 2.0.1   2014-10-29 CRAN (R 3.1.2)
 raster       2.3-40  2015-04-11 CRAN (R 3.1.3)
 Rcpp       * 0.11.6  2015-05-01 CRAN (R 3.1.3)
 reshape2   * 1.4.1   2014-12-06 CRAN (R 3.1.2)
 roxygen2     5.0.0   2015-10-28 CRAN (R 3.1.3)
 rstudioapi * 0.3.1   2015-04-07 CRAN (R 3.1.3)
 scales     * 0.3.0   2015-08-25 CRAN (R 3.1.3)
 sp           1.1-0   2015-04-24 CRAN (R 3.1.3)
 stringi    * 0.4-1   2014-12-14 CRAN (R 3.1.2)
 stringr    * 1.0.0   2015-04-30 CRAN (R 3.1.3)


> ls(roxygen2:::tags)
 [1] "aliases"           "author"            "backref"           "concept"          
 [5] "describeIn"        "description"       "details"           "docType"          
 [9] "encoding"          "evalRd"            "example"           "examples"         
[13] "export"            "exportClass"       "exportMethod"      "exportPattern"    
[17] "family"            "field"             "format"            "import"           
[21] "importClassesFrom" "importFrom"        "importMethodsFrom" "include"          
[25] "inheritParams"     "keywords"          "method"            "name"             
[29] "noRd"              "note"              "param"             "rawNamespace"     
[33] "rawRd"             "rdname"            "references"        "return"           
[37] "S3method"          "section"           "seealso"           "slot"             
[41] "source"            "template"          "templateVar"       "title"            
[45] "usage"             "useDynLib"        

hadley added a commit that referenced this issue Nov 2, 2015
@hadley
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@hadley hadley commented Nov 2, 2015

@emhart can you try now? I just spotted a really dumb error so I think it might be ok for you now

@hadley
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@hadley hadley commented Nov 2, 2015

Nope, I just don't understand operator precedence.

@hadley
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@hadley hadley commented Nov 2, 2015

Any chance you have an object called tags in your global environment or package?

@kevinushey
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@kevinushey kevinushey commented Nov 3, 2015

I know what's going on (and I was just bitten by this in packrat as well!)

You're using names(tags) to try and get items within an environment, but the names method only exists for environments with R >= 3.2. You need to use ls(tags) instead.

@hadley hadley closed this in 5c054aa Nov 3, 2015
hadley added a commit that referenced this issue Nov 3, 2015
use 'ls()' instead of 'names()' (closes #422)
@Starfox899
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@Starfox899 Starfox899 commented Nov 3, 2015

I can confirm this fixed the bug. I checked latest git version, and now it works fine.
Thanks a lot!

@fisher
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@fisher fisher commented Nov 5, 2015

And when the fix will be available through install.package() ?

@christophergandrud
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@christophergandrud christophergandrud commented Jan 31, 2017

I just upgraded to version 6.0.0 and am now getting a similar series of warnings for a package's reference class documentation, e.g.:

Updating Zelig documentation
Loading Zelig
Warning: @import [model-zelig.R#6]: unknown tag
Warning: @export [model-zelig.R#7]: unknown tag
Warning: @exportClass [model-zelig.R#8]: unknown tag
Warning: @import [model-timeseries.R#4]: unknown tag
Warning: @export [model-timeseries.R#5]: unknown tag
Warning: @exportClass [model-timeseries.R#6]: unknown tag
Warning: @export [model-timeseries.R#150]: unknown tag
Warning: @import [model-ma.R#5]: unknown tag
Warning: @export [model-ma.R#6]: unknown tag
Warning: @exportClass [model-ma.R#7]: unknown tag
Warning: @import [model-ar.R#5]: unknown tag
Warning: @export [model-ar.R#6]: unknown tag
Warning: @exportClass [model-ar.R#7]: unknown tag

and so on.

Any idea what's going on. (I'ld be happy to provide sessionInfo, etc if that would help.)

@hadley
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@hadley hadley commented Jan 31, 2017

@christophergandrud can you please file a new issue with a minimal reprex?

@christophergandrud
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@christophergandrud christophergandrud commented Jan 31, 2017

Sure. New issue at: #571

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