Bug: `Error in loadNamespace(name) : there is no package called ‘pkg’` when running `pkgdown::build_site()`

[talgalili]

Reproduce (while working on the dendextend package):

>  pkgdown::build_site()
-- Installing package into temporary library -------------------------------------------------
== Building pkgdown site =======================================================
Reading from: '/home/talgalili/Dropbox/aaaa good R code/AA - My packages/dendextend'
Writing to:   '/home/talgalili/Dropbox/aaaa good R code/AA - My packages/dendextend/docs'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Writing 'authors.html'
Reading 'CONDUCT.md'
Writing 'CONDUCT.html'
Error in loadNamespace(name) : there is no package called ‘pkg’
Error: callr subprocess failed: there is no package called ‘pkg’
Type .Last.error.trace to see where the error occurred

`sessionInfo()` log (notice that this is an old R: 3.6.3, on linux MINT 19.2)
 
--
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 19.2

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
 [1] LC_CTYPE=en_IL.UTF-8       LC_NUMERIC=C               LC_TIME=en_IL.UTF-8       
 [4] LC_COLLATE=en_IL.UTF-8     LC_MONETARY=en_IL.UTF-8    LC_MESSAGES=en_IL.UTF-8   
 [7] LC_PAPER=en_IL.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_IL.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] pkgdown_2.0.5     dendextend_1.16.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2  xfun_0.21         remotes_2.2.0     purrr_0.3.4       colorspace_2.0-0 
 [6] vctrs_0.4.1       generics_0.1.0    htmltools_0.5.2   viridisLite_0.3.0 yaml_2.2.1       
[11] utf8_1.1.4        rlang_1.0.3       pillar_1.7.0      glue_1.6.2        withr_2.5.0      
[16] DBI_1.1.1         lifecycle_1.0.1   munsell_0.5.0     gtable_0.3.0      memoise_2.0.0    
[21] evaluate_0.14     knitr_1.31        callr_3.7.0       fastmap_1.1.0     ps_1.5.0         
[26] curl_4.3          fansi_0.4.2       scales_1.1.1      cachem_1.0.4      desc_1.2.0       
[31] jsonlite_1.7.2    fs_1.5.0          gridExtra_2.3     ggplot2_3.3.3     digest_0.6.27    
[36] processx_3.6.1    dplyr_1.0.9       grid_3.6.3        rprojroot_2.0.2   cli_3.3.0        
[41] tools_3.6.3       magrittr_2.0.1    tibble_3.1.7      crayon_1.4.1      whisker_0.4      
[46] pkgconfig_2.0.3   downlit_0.4.1     ellipsis_0.3.2    xml2_1.3.2        assertthat_0.2.1 
[51] rmarkdown_2.7     httr_1.4.2        rstudioapi_0.13   viridis_0.5.1     R6_2.5.0         
[56] compiler_3.6.3   

[dmurdoch]

What does .Last.error.trace show you?

[dmurdoch]

In your README.md, you have this:

install.packages.2 <- function (pkg) if (!require(pkg)) install.packages(pkg);

I think that should have been

install.packages.2 <- function (pkg) if (!requireNamespace(pkg)) install.packages(pkg);

because normally you don't want to add things to the search list. But if you really want to use require(), you need the character.only = TRUE argument so that it doesn't try to load the package named "pkg".

[talgalili]

Interesting, let me take a look :)

[talgalili]

Output

> .Last.error.trace

 Stack trace:

 Process 17264:
 1. pkgdown::build_site()
 2. pkgdown:::build_site_external(pkg = pkg, examples = examples,  ...
 3. callr::r(function(..., crayon_enabled, crayon_colors, pkgdown_internet) { ...
 4. callr:::get_result(output = out, options)
 5. throw(newerr, parent = remerr[[2]])

 x callr subprocess failed: there is no package called ‘pkg’ 

 Process 17386:
 17. (function (..., crayon_enabled, crayon_colors, pkgdown_internet)  ...
 18. pkgdown::build_site(...)
 19. pkgdown:::build_site_local(pkg = pkg, examples = examples, run_dont_run = r ...
 20. pkgdown:::build_home(pkg, override = override, preview = FALSE)
 21. pkgdown:::build_home_index(pkg, quiet = quiet)
 22. pkgdown:::render_page(pkg, "home", data, "index.html", quiet = quiet)
 23. pkgdown:::tweak_page(html, name, pkg = pkg)
 24. downlit::downlit_html_node(html)
 25. downlit:::tweak_children(x, xpath_block, highlight, pre_class = "downlit so ...
 26. downlit:::map_chr(text, fun, ...)
 27. base:::vapply(.x, .f, ..., FUN.VALUE = character(1), USE.NAMES = FALSE)
 28. downlit:::FUN(X[[i]], ...)
 29. downlit:::token_href(out$token, out$text)
 30. downlit:::map_chr(text[fun], href_topic_local, is_fun = TRUE)
 31. base:::vapply(.x, .f, ..., FUN.VALUE = character(1), USE.NAMES = FALSE)
 32. downlit:::FUN(X[[i]], ...)
 33. downlit:::find_rdname_attached(topic, is_fun = is_fun)
 34. downlit:::is_exported(topic, package)
 35. base:::`%in%`(name, getNamespaceExports(ns_env(package)))
 36. base:::getNamespaceExports(ns_env(package))
 37. base:::asNamespace(ns)
 38. rlang:::ns_env(package)
 39. base:::asNamespace(x)
 40. base:::getNamespace(ns)
 41. base:::loadNamespace(name)
 42. base:::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 43. base:::withOneRestart(expr, restarts[[1L]])
 44. base:::doWithOneRestart(return(expr), restart)
 45. base:::stop(cond)
 46. (function (e)  ...

 x there is no package called ‘pkg’ 

[dmurdoch]

That error is coming from downlit, which wants to make a link to some topic, probably on the pkg website.

[talgalili]

Changing to use: install.packages.2 <- function (pkg) if (!require(pkg, character.only = TRUE)) Seems to have solved it.

It still crashes (but because I'm missing a package). Is there a way to force skip it when this happens, instead of letting it crash?

>  pkgdown::build_site()
-- Installing package into temporary library -------------------------------------------------
== Building pkgdown site =======================================================
Reading from: '/home/talgalili/Dropbox/aaaa good R code/AA - My packages/dendextend'
Writing to:   '/home/talgalili/Dropbox/aaaa good R code/AA - My packages/dendextend/docs'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Reading 'CONDUCT.md'
Writing '404.html'
-- Building function reference -------------------------------------------------
|
---------------------
Welcome to dendextend version 1.16.0
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
You may ask questions at stackoverflow, use the r and dendextend tags: 
     https://stackoverflow.com/questions/tagged/dendextend

    To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
---------------------

/
Attaching package: ‘dendextend’

The following object is masked from ‘package:stats’:

    cutree

Reading 'man/Bk.Rd'
Reading 'man/Bk_permutations.Rd'
Reading 'man/Bk_plot.Rd'
Reading 'man/DendSer.dendrogram.Rd'
Registered S3 method overwritten by 'seriation':
  method         from 
  reorder.hclust gclus
Reading 'man/FM_index.Rd'
Reading 'man/FM_index_R.Rd'
Reading 'man/FM_index_permutation.Rd'
Error in .f(.x[[i]], ...) : Failed to parse Rd in FM_index_permutation.Rd
ℹ there is no package called ‘psych’
Caused by error in `loadNamespace()`:
! there is no package called ‘psych’
Error: callr subprocess failed: Failed to parse Rd in FM_index_permutation.Rd
ℹ there is no package called ‘psych’
Caused by error in `loadNamespace()`:
! there is no package called ‘psych’
Type .Last.error.trace to see where the error occurred

(I can't seem to install psych, but that's another issue, unrelated to pkgdown)

[talgalili]

And thanks a lot @dmurdoch for the super fast and helpful responses!

[dmurdoch]

I think the psych issue might be fixed in the devel version of downlit, by this commit: https://github.com/r-lib/downlit/commit/24ccb0b5d41a80583b1c998077fe528dd6c5af16 .

[talgalili]

I take it back, I think the bug still occurs even after moving to use the following in README.md:

install.packages.2 <- function (pkg) {
   if (!require(pkg, character.only = TRUE)) 
   install.packages(pkg, character.only = TRUE)
   }

Output

> pkgdown::build_home()
-- Building home ------------------------------------------------------------------------------
Reading 'CONDUCT.md'
Error in loadNamespace(name) : there is no package called ‘pkg’

[dmurdoch]

I think there are issues in downlit still. In particular, autolink_url() calls href_expr, and it doesn't handle library, require and requireNamespace properly. I suspect that's where the problem arises. I'll open an issue there...