pkgdown 1.1.0 does not process \doi tags

[strengejacke]

When I use build_site() with my package (https://github.com/strengejacke/sjstats), I get following error for pkgdown 1.1.0:

Reading 'man/deff.Rd'
Error: x must be a string or a R connection
Execution halted

Reverting to pkgdown 1.0.0 solves the problem, there's no error then.

[jayhesselberth]

One problem is the \doi tag. A minimal package with only the file:

#' \doi{blah}
test <- function() {}

triggers Error: x must be a string or a R connection.

For reference:

devtools::load_all("~/devel/pkgdown")
#> Loading pkgdown

rd_text("\\doi{10.1177/0163278703255230}")
#> \Sexpr[results=rd,stage=build]{tools:::Rd_expr_doi("#1")}10.1177/0163278703255230[results=rd,stage=build]{tools:::Rd_expr_doi("10.1177/0163278703255230")}

tools:::Rd_expr_doi("10.11177/0163278703255230")
#> [1] "\\ifelse{text}{doi: 10.11177/0163278703255230 (URL: http://doi.org/10.11177/0163278703255230)}{\\ifelse{latex}{doi:\\out{\\nobreakspace{}}\\href{http://doi.org/10.11177/0163278703255230}{10.11177\\out{\\slash{}}0163278703255230}}{doi: \\href{http://doi.org/10.11177/0163278703255230}{10.11177/0163278703255230}}}"

# rd2html deals with this OK
rd2html(tools:::Rd_expr_doi("10.11177/0163278703255230"))
#> [1] "doi: <a href='http://doi.org/10.11177/0163278703255230'>10.11177/0163278703255230</a>"

Created on 2018-06-15 by the reprex package (v0.2.0).

[strengejacke]

I haven't checked systematically yet, but I can confirm that for all .rd-file I remember where an error occured, these also contained a doi-tag.

[aqualogy]

In the meantime I have also prepared an example package:

https://github.com/aqualogy/pdtest720

First I suspected the Rdpack macro \insertRef as error source, but in the meantime I can confirm the Rd-files \doi tag as error source, too. During execution of _build.R build_site() fails for df.flys4.Rd, which is the first of five variations of df.flys?.Rd that includes the \doi tag. The three previous versions (df.flys1.Rd, df.flys2.Rd, df.flys3.Rd) work well, the later two with \doi tag or \insertRef tag fail.

@KasperSkytte Since I used to explicitely overwrite the destination of the output to a subdirectory of public/ (Gitlab's standard directory for static html output) depending on the R version (public/R-3.5.0/), I didn't expect to get a directory docs/ produced by build_site(). In the meantime I have reported this as separate issue: #734

[KasperSkytte]

I removed \doi{} tags and now it runs perfectly. Who would have known. Thanks for the quick responses!

[strengejacke]

so what has changed with the parsing, as all works well in version 1.0.0?

[jayhesselberth]

Hmm, good question. Your DOI links were previously linked just fine using 1.0.0.

https://strengejacke.github.io/sjstats/reference/deff.html#references

It's most likely a change in rd-html.R between v1.0.0...v1.1.0

This test needs to pass:

test_that("DOIs are linked", {
  expect_equal(
    rd2html("\\doi{10.1177/0163278703255230}"),
    "doi: <a href='http://doi.org/10.11177/0163278703255230'>10.11177/0163278703255230</a>"
  )
})

[aravind-j]

The tag \insertRef of the Rd macro Rdpack is also not parsed and generates the same error.

[jayhesselberth]

\doi should be fixed by #738. Can someone confirm whether \insertRef is also fixed?

[aqualogy]

Not yet! After updating to current master (devtools::install_github("R-lib/pkgdown")) I still get an error at the first occurences of \doi and \insertRef.

sessionInfo()

R version 3.5.0 (2018-04-23) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] rmarkdown_1.10 knitr_1.20 devtools_1.13.5 pdtest720_0.1.0
[5] pkgdown_1.1.0.9000

loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 xml2_1.2.0 magrittr_1.5 roxygen2_6.0.1
[5] MASS_7.3-50 debugme_1.1.0 R6_2.2.2 rlang_0.2.1
[9] bibtex_0.4.2 stringr_1.3.1 tools_3.5.0 withr_2.1.2
[13] htmltools_0.3.6 commonmark_1.5 yaml_2.1.19 assertthat_0.2.0
[17] digest_0.6.15 rprojroot_1.3-2 tibble_1.4.2 crayon_1.3.4
[21] processx_3.1.0 callr_2.0.4 purrr_0.2.5 Rdpack_0.8-0
[25] fs_1.2.3 gbRd_0.4-11 memoise_1.1.0 evaluate_0.10.1
[29] stringi_1.2.3 compiler_3.5.0 pillar_1.2.3 desc_1.2.0
[33] backports_1.1.2

traceback

5: stop(err[[2]]) 4: get_result(output = out, options) 3: callr::r(function(...) pkgdown::build_site(...), args = args, show = TRUE) 2: build_site_external(pkg = pkg, examples = examples, document = document, run_dont_run = run_dont_run, seed = seed, mathjax = mathjax, lazy = lazy, override = override, preview = preview) 1: pkgdown::build_site(".")

[strengejacke]

thanks, works for me now!

[gvegayon]

Same here! Thanks!

[pachadotdev]

same here
what solved the problem for me was

library(devtools)
install_version("pkgdown", version = "1.0.0", repos = "http://cran.us.r-project.org")

[KasperSkytte]

It's fixed in the latest development version. Just install it with devtools::install_github("r-lib/pkgdown"), not the one from CRAN as it is not up to date.

[aqualogy]

I can confirm @KasperSkytte last comment. With current master, installed by devtools::install_github("r-lib/pkgdown") everything works well and \insertRef or \doi don't cause problems.