Roxygen2: Request: make missing link warnings more verbose

[mjsteinbaugh]

Hi, I'm seeing this warning now pop up in roxygen2 for one of my packages:

Warning: Link to unknown topic in inherited text: methods::StructureClasses

I'm having trouble locating the source of this warning. Is there a way we can tweak roxygen2 to return which Rd file and line in particular is causing the issue?

[mjsteinbaugh]

Is pull #1109 potentially related?

[gaborcsardi]

Is there a way we can tweak roxygen2 to return which Rd file and line in particular is causing the issue?

Maybe, but you can also search for StructureClasses in your Rd files for now?

[mjsteinbaugh]

Hi @gaborcsardi , just figured it out.

I was using this line to inherit some params from as_tibble documentation:

#' @inheritParams tibble::as_tibble

Taking this out gets rid of the warning. I think it may have to do with this Rd code being linked:

\item{rownames}{How to treat existing row names of a data frame or matrix:
\itemize{
\item \code{NULL}: remove row names. This is the default.
\item \code{NA}: keep row names.
\item A string: the name of a new column. Existing rownames are transferred
into this column and the \code{row.names} attribute is deleted.
Read more in \link[tibble]{rownames}.
}}

Not sure how that goes up the stack to result in the StructureClasses warning.

See related commit in pipette package for details.

[gaborcsardi]

Interesting. I'll reopen this, because it seems to be a bug if StructureClasses is not used in the Rd at all.

[mjsteinbaugh]

I'm hitting this issue again with another package, and the warning is time consuming to debug. This time I'm hitting:

Warning: Link to unknown topic in inherited text: stats::bandwidth

And I have no idea which Rd file this link is being pulled from. If there is a way to add a traceback for the link failure, it would be super helpful.

[mjsteinbaugh]

In case anyone else hits an issue like this, here's the link problem I hit:

https://github.com/acidgenomics/pointillism/blob/v0.4.12/R/plotCounts-methods.R#L11

#' @inheritParams ggplot2::geom_violin

[dmurdoch]

This seems related: I want to add a Note to the pkgbuild::build documentation containing a link to devtools::submit_cran.

But devtools::build has @inherit pkgbuild::build, so processing devtools triggers a series of warnings Warning: Link to unknown topic in inherited text: devtools::submit_cran. This happens even though the Note would not be inherited, according to the docs at https://github.com/r-lib/roxygen2/blob/513c9e25262e67e7d3383a0feb51be0ba9b6e21f/vignettes/rd.Rmd#L436

[baderstine]

@mjsteinbaugh this is newly happening in one of my packages. How did you find the source of it?

[mjsteinbaugh]

@baderstine It's a tough thing to track down. I've been looking through the Rd documentation files manually until I spot the problem.

[phargarten2]

@mjsteinbaugh I recently updated all dependent packages and updated the R version to the latest version, v. 4.0.5. Using devtools::document(), the warning mentioned above is now coming up in the new version of roxygen2 (7.1.1) that it didn't before.

Warning: Link to unknown topic in inherited text: tools::print.via.format

print.via.format() did not show up in any Rd file.

Session Info:

R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16, RStudio 1.2.1335

Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8

Package version:
  askpass_1.1              assertthat_0.2.1         backports_1.2.1          base64enc_0.1-3         
  BH_1.75.0.0              brew_1.0.6               brio_1.1.1               cachem_1.0.4            
  callr_3.6.0              checkmate_2.0.0          cli_2.3.1                clipr_0.7.1             
  cluster_2.1.1            coda_0.19-4              colorspace_2.0-0         commonmark_1.7          
  compiler_4.0.5           condMVNorm_2020.1        conquer_1.0.2            covr_3.5.1              
  cpp11_0.2.7              crayon_1.4.1             credentials_1.3.0        crosstalk_1.1.1         
  curl_4.3                 data.table_1.14.0        desc_1.3.0               devtools_2.3.2          
  diffobj_0.3.4            digest_0.6.27            dplyr_1.0.5              DT_0.17                 
  ellipsis_0.3.1           evaluate_0.14            fansi_0.4.2              farver_2.1.0            
  fastmap_1.1.0            foreign_0.8-81           Formula_1.2-4            fs_1.5.0                
  generics_0.1.0           gert_1.3.0               ggplot2_3.3.3            gh_1.2.1                
  gitcreds_0.1.1           glm2_1.2.1               glue_1.4.2               gmm_1.6-6               
  graphics_4.0.5           grDevices_4.0.5          grid_4.0.5               gridExtra_2.3           
  gtable_0.3.0             highr_0.8                Hmisc_4.5-0              htmlTable_2.1.0         
  htmltools_0.5.1.1        htmlwidgets_1.5.3        httr_1.4.2               ini_0.3.1               
  invgamma_1.1             isoband_0.2.4            jpeg_0.1-8.1             jsonlite_1.7.2          
  knitr_1.31               labeling_0.4.2           later_1.1.0.1            lattice_0.20-41         
  latticeExtra_0.6-29      lazyeval_0.2.2           lifecycle_1.0.0          magrittr_2.0.1          
  markdown_1.1             MASS_7.3-53.1            Matrix_1.3-2             MatrixModels_0.5-0      
  matrixNormal_0.0.4       matrixStats_0.58.0       mcmc_0.9-7               MCMCpack_1.5-0          
  memoise_2.0.0            methods_4.0.5            mgcv_1.8.34              mime_0.10               
  miWQS_0.4.5              munsell_0.5.0            mvtnorm_1.1-1            nlme_3.1.152            
  nnet_7.3-15              openssl_1.4.3            parallel_4.0.5           pillar_1.5.1            
  pkgbuild_1.2.0           pkgconfig_2.0.3          pkgload_1.2.0            png_0.1-7               
  praise_1.0.0             prettyunits_1.1.1        processx_3.5.0           promises_1.2.0.1        
  ps_1.6.0                 purrr_0.3.4              quantreg_5.85            R6_2.5.0                
  rappdirs_0.3.3           rcmdcheck_1.3.3          RColorBrewer_1.1-2       Rcpp_1.0.6              
  RcppArmadillo_0.10.2.2.0 rematch2_2.1.2           remotes_2.3.0            rex_1.2.0               
  rlang_0.4.10             rlist_0.4.6.1            roxygen2_7.1.1           rpart_4.1-15            
  rprojroot_2.0.2          Rsolnp_1.16              rstudioapi_0.13          rversions_2.0.2         
  sandwich_3.0-0           scales_1.1.1             sessioninfo_1.1.1        SparseM_1.81            
  splines_4.0.5            stats_4.0.5              stats4_4.0.5             stringi_1.5.3           
  stringr_1.4.0.9000       survival_3.2-10          sys_3.4                  testthat_3.0.2          
  tibble_3.1.0             tidyr_1.1.3              tidyselect_1.1.0         tmvmixnorm_1.1.1        
  tmvtnorm_1.4-10          tools_4.0.5              truncnorm_1.0-8          usethis_2.0.1           
  utf8_1.2.1               utils_4.0.5              vctrs_0.3.7              viridis_0.5.1           
  viridisLite_0.3.0        waldo_0.2.5              whisker_0.4              withr_2.4.1             
  xfun_0.22                XML_3.99.0.6             xml2_1.3.2               xopen_1.0.0             
  yaml_2.2.1               zip_2.1.1                zoo_1.8-9               

[ColinFay]

I'm getting the same as @phargarten2.

> devtools::document()
ℹ Updating golem documentation
ℹ Loading golem
Writing NAMESPACE
Warning: Link to unknown topic in inherited text: tools::print.via.format
Writing NAMESPACE
>
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] golem_0.3.1

loaded via a namespace (and not attached):
 [1] xfun_0.22         remotes_2.3.0     purrr_0.3.4       rcmdcheck_1.3.3   vctrs_0.3.7      
 [6] testthat_3.0.2    usethis_2.0.1     htmltools_0.5.1.1 yaml_2.2.1        utf8_1.2.1       
[11] rlang_0.4.10      pkgbuild_1.2.0    later_1.1.0.1     pillar_1.5.1      glue_1.4.2       
[16] withr_2.4.1       xopen_1.0.0       sessioninfo_1.1.1 lifecycle_1.0.0   stringr_1.4.0    
[21] commonmark_1.7    devtools_2.4.0    memoise_2.0.0     knitr_1.31        callr_3.6.0      
[26] fastmap_1.1.0     httpuv_1.5.5      ps_1.6.0          fansi_0.4.2       Rcpp_1.0.6       
[31] xtable_1.8-4      promises_1.2.0.1  cachem_1.0.4      desc_1.3.0        pkgload_1.2.1    
[36] jsonlite_1.7.2    debugme_1.1.0     config_0.3.1      mime_0.10         fs_1.5.0         
[41] digest_0.6.27     stringi_1.5.3     processx_3.5.1    shiny_1.6.0       rprojroot_2.0.2  
[46] here_1.0.1        cli_2.4.0         tools_4.0.5       magrittr_2.0.1    dockerfiler_0.1.3
[51] tibble_3.1.0      crayon_1.4.1      pkgconfig_2.0.3   ellipsis_0.3.1    xml2_1.3.2       
[56] prettyunits_1.1.1 attempt_0.3.1     roxygen2_7.1.1    rstudioapi_0.13   R6_2.5.0         
[61] compiler_4.0.5 

[jatkins23]

I have the same error but the source is @inheritDotParams dplyr::as_tibble and the missing topic is magrittr::pipe which seems pretty clearly documented and included in my package. @mjsteinbaugh, not sure I understood your follow up but were you able to remove this error?

[mjsteinbaugh]

@jatkins23 Still an unresolved issue, unfortunately! What I started doing in my code is intentionally avoid linking to package documentation that I don't write myself. This helps avoid breaking changes that are then hard to debug currently with roxygen2.