Usethis: `usethis::use_pipe()` gives `.Rd` warning
After using usethis::use_pipe() in my R package, roxygen2::roxygenize() has started producing the following warning:
file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
How can I get rid of it? Or, even better, is there any way that the usethis function can be modified so that it produces the roxygen template for %>% that doesn't produce this warning?
IndrajeetPatil
All 15 comments
Had this happen too. I first could not follow the suggested instructions of running devtools::document() after usethis::use_pipe() - RStudio would crash completely. The only way I could run it is in a command line R session, after which I receive the same warning when running devtools::document().
kdaily
on 6 Oct 2018
Can either of you provide a clean reprex? I can't reproduce your problem.
Using the current dev version of usethis (1e3c6a66e8b2d2790ee6d7e6d5651c52fb61abfc):
I execute usethis::create_package("~/tmp/zzz").
In the new package zzz, I see this:
> use_roxygen_md()
✔ Setting active project to '/Users/jenny/tmp/zzz'
✔ Setting Roxygen field in DESCRIPTION to 'list(markdown = TRUE)'
✔ Setting RoxygenNote field in DESCRIPTION to '6.1.0'
● Run `devtools::document()`
> use_pipe()
✔ Adding 'magrittr' to Imports field in DESCRIPTION
✔ Writing 'R/utils-pipe.R'
● Run `devtools::document()`
> devtools::document()
Updating zzz documentation
Writing NAMESPACE
Loading zzz
Writing NAMESPACE
Writing pipe.Rd
Here's my version of devtools and roxygen2:
devtools * 1.13.6.9000 2018-10-06 [1] Github (r-lib/devtools@c24b146)
roxygen2 6.1.0 2018-07-27 CRAN (R 3.5.0)
jennybc
on 6 Oct 2018
Huh, if I try to do a reprex, I don't get any warning in the reprex.
setwd("~/sentiwordcloud")
usethis::use_roxygen_md()
#> <U+2714> Setting active project to 'C:/Users/inp099/Documents/sentiwordcloud'
#> Error: Package 'roxygen2md' required. Please install before re-trying.
usethis::use_pipe()
#> <U+25CF> Run `devtools::document()`
devtools::document()
#> Updating sentiwordcloud documentation
#> Writing NAMESPACE
#> Loading sentiwordcloud
#> Writing NAMESPACE
devtools::document(roclets = c('rd', 'collate', 'namespace'))
#> Updating sentiwordcloud documentation
#> Writing NAMESPACE
#> Loading sentiwordcloud
#> Writing NAMESPACE
Created on 2018-10-05 by the reprex package (v0.2.1)
But I still get this warning in my local session.
Here is my session info:
options(width = 200)
devtools::session_info()
#> - Session info ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#> setting value
#> version R version 3.5.1 (2018-07-02)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/New_York
#> date 2018-10-05
#>
#> - 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)
#> 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)
#> crayon 1.3.4 2018-09-26 [1] Github (r-lib/crayon@3e751fb)
#> debugme 1.1.0 2017-10-22 [1] CRAN (R 3.5.0)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
#> devtools 1.13.6.9000 2018-09-23 [1] Github (r-lib/devtools@74df201)
#> digest 0.6.17 2018-09-12 [1] CRAN (R 3.5.1)
#> evaluate 0.11 2018-07-17 [1] CRAN (R 3.5.1)
#> fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.1)
#> glue 1.3.0 2018-09-17 [1] Github (tidyverse/glue@4e74901)
#> htmldeps 0.1.1 2018-09-17 [1] Github (rstudio/htmldeps@c1023e0)
#> htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.0)
#> knitr 1.20.12 2018-08-13 [1] local
#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.0)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.0)
#> pkgbuild 1.0.1.9000 2018-10-01 [1] Github (r-lib/pkgbuild@446d70c)
#> pkgload 1.0.0 2018-09-17 [1] Github (r-lib/pkgload@7771d78)
#> prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.0)
#> processx 3.2.0 2018-08-16 [1] CRAN (R 3.5.1)
#> ps 1.1.0 2018-08-10 [1] CRAN (R 3.5.1)
#> R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.1)
#> Rcpp 0.12.19 2018-10-01 [1] CRAN (R 3.5.1)
#> remotes 1.1.1.9000 2018-09-23 [1] Github (r-lib/remotes@5a07ad2)
#> rlang 0.2.2 2018-08-16 [1] CRAN (R 3.5.1)
#> rmarkdown 1.10.13 2018-09-17 [1] Github (rstudio/rmarkdown@df4ec91)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
#> sessioninfo 1.1.0 2018-09-25 [1] CRAN (R 3.5.1)
#> 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 2.0.0 2017-12-13 [1] CRAN (R 3.5.0)
#> usethis 1.4.0.9000 2018-09-23 [1] Github (r-lib/usethis@1e3c6a6)
#> withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
#> xfun 0.3 2018-07-06 [1] CRAN (R 3.5.1)
#> yaml 2.2.0 2018-07-25 [1] CRAN (R 3.5.1)
#>
#> [1] C:/Users/inp099/Documents/R/win-library/3.5
#> [2] C:/Program Files/R/R-3.5.1/library
Created on 2018-10-05 by the reprex package (v0.2.1)
IndrajeetPatil
on 6 Oct 2018
> usethis::create_package("usethisissue478") # restarts R normally
> usethis::use_roxygen_md()
✔ Setting active project to '/home/kdaily/scratch/usethisissue478'
✔ Setting Roxygen field in DESCRIPTION to 'list(markdown = TRUE)'
✔ Setting RoxygenNote field in DESCRIPTION to '6.1.0'
● Run `devtools::document()`
> devtools::document()
Updating usethisissue478 documentation
Loading usethisissue478
Writing NAMESPACE
> usethis::use_pipe()
✔ Adding 'magrittr' to Imports field in DESCRIPTION
✔ Writing 'R/utils-pipe.R'
● Run `devtools::document()`
> devtools::document()
Updating usethisissue478 documentation
Loading usethisissue478
results in RStudio modal popup:
R Session Aborted
R encountered a fatal error.
The session was terminated.
I started a new R session and re-created the package (using only usethis::create_package("usethisissue478"). After reloading, this was my sessionInfo:
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 27 (Workstation Edition)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0 yaml_2.1.19
I have usethis 1.4.0, magrittr 1.5, and RStudio 1.1.383.
kdaily
on 8 Oct 2018
Can you both report what version of roxygen2 you have?
jennybc
on 8 Oct 2018
I have roxygen2 6.1.0.
kdaily
on 8 Oct 2018
I have:
roxygen2 6.1.0.9000
roxygen2md 0.0.4.9000
This doesn't solve the issue, but shouldn't \code{magrittr::\link[magrittr]{\%>\%}} here be \code{\link[magrittr]{\%>\%}}?
#' Pipe operator
#'
#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
#'
#' @name %>%
#' @rdname pipe
#' @keywords internal
#' @export
#' @importFrom magrittr %>%
#' @usage lhs \%>\% rhs
NULL
The same also holds true for the roxygen template created by usethis::use_tibble().
IndrajeetPatil
on 5 Nov 2018
No, I think the text and link are what we want them to be.
jennybc
on 5 Nov 2018
Hmm, this doesn't seem specific to the pipe operator. For example, if re-export some of the tidyverse operators-
#' @export
#' @importFrom rlang "%||%"
rlang::`%||%`
#' @export
#' @importFrom rlang "%|%"
rlang::`%|%`
#' @export
#' @importFrom magrittr "%>%"
magrittr::`%>%`
#' @export
#' @importFrom magrittr "%<>%"
magrittr::`%<>%`
#' @export
#' @importFrom magrittr "%$%"
magrittr::`%$%`
All of these provide warnings during devtools::check():
Rd warning: C:/Users/inp099/Documents/ggstatsplot/man/reexports.Rd:22: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/inp099/Documents/ggstatsplot/man/reexports.Rd:22: file link '%<>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/inp099/Documents/ggstatsplot/man/reexports.Rd:22: file link '%$%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/inp099/Documents/ggstatsplot/man/reexports.Rd:24: file link '%||%' in package 'rlang' does not exist and so has been treated as a topic
So maybe the issue is with roxygen2 and how it is handling operators with unusual names?
IndrajeetPatil
on 12 Nov 2018
This is not a usethis problem, but is somehow related to your version of R. The warning can be ignored.
hadley
on 24 Nov 2018
@hadley is there somewhere else I should report this? This crashes RStudio for me (see https://github.com/r-lib/usethis/issues/478#issuecomment-427879907). Thanks!
kdaily
on 26 Nov 2018
I doubt that is the source of the crash. Maybe start in community.rstudio.com?
hadley
on 26 Nov 2018
Will do. Thanks!
kdaily
on 26 Nov 2018
I believe the issue can be solved temporarily by modifying the doc string from
#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
to
#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
The reason is that we need to indicate the .Rd file name (in this case pipe) that contains the topic %>%. See also https://github.com/klutometis/roxygen/issues/707
MikeBadescu
on 31 Dec 2018
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Most helpful comment
I believe the issue can be solved temporarily by modifying the doc string from
to
The reason is that we need to indicate the
.Rdfile name (in this casepipe) that contains the topic%>%. See also https://github.com/klutometis/roxygen/issues/707