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librdf error - HTML parser error: Tag #106

Closed
oggioniale opened this issue Nov 29, 2023 · 17 comments
Closed

librdf error - HTML parser error: Tag #106

oggioniale opened this issue Nov 29, 2023 · 17 comments

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@oggioniale
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executing rotemplate::build_ropensci_docs(path = ".") for the package ReLTER I have some errors like this:

> rotemplate::build_ropensci_docs(path = ".")
Site needs mathjax library
== Building pkgdown site =======================================================
Reading from: '/xxx/ReLTER'
Writing to:   '/xxx/ReLTER/docs'
-- Initialising site -----------------------------------------------------------
-- Building home ---------------------------------------------------------------
Reading 'CONTRIBUTING.md'
Reading 'LICENSE.md'
Writing '404.html'
-- Building function reference -------------------------------------------------
Writing 'reference/index.html'
-

ReLTER is specially drafted for the LTER community.

To contribute to the improvement of this package, join the group of
    developers (https://github.com/ropensci/ReLTER).

If you use this package, please cite as:

Alessandro Oggioni, Micha Silver, Luigi Ranghetti & Paolo Tagliolato.
    (2023) ReLTER: An Interface for the eLTER Community (v2.1). Zenodo.
    https://doi.org/10.5281/zenodo.5576813

Type 'citation(package = 'ReLTER')' on how to cite R packages in
    publications.

Currently the DEIMS-SDR base URL is set as: https://deims.org/.
To change the URL please use set_deims_base_url().
Reading 'man/ReLTER-package.Rd'
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag main invalid
librdf error - HTML parser error: Tag aside invalid
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag footer invalid
Reading 'man/do_Q.Rd'
Reading 'man/elter_write_rdata.Rd'
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag main invalid
librdf error - HTML parser error: Tag aside invalid
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag footer invalid
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag main invalid
librdf error - HTML parser error: Tag aside invalid
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag footer invalid
Reading 'man/get_activity_info.Rd'
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag main invalid
librdf error - HTML parser error: Tag aside invalid
librdf error - HTML parser error: Tag nav invalid
librdf error - HTML parser error: Tag footer invalid
...
Session Info 
> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.0 (2023-04-21)
 os       macOS 14.0
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Rome
 date     2023-11-29
 rstudio  2023.06.0+421 Mountain Hydrangea (desktop)
 pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 !  package       * version    date (UTC) lib source
    abind           1.4-5      2016-07-21 [1] CRAN (R 4.3.0)
    ape             5.7-1      2023-03-13 [1] CRAN (R 4.3.0)
    assertthat      0.2.1      2019-03-21 [1] CRAN (R 4.3.0)
    atom4R          0.3-3      2022-11-18 [1] CRAN (R 4.3.0)
    backports       1.4.1      2021-12-13 [2] CRAN (R 4.3.0)
    base64enc       0.1-3      2015-07-28 [2] CRAN (R 4.3.0)
    bit             4.0.5      2022-11-15 [2] CRAN (R 4.3.0)
    bit64           4.0.5      2020-08-30 [2] CRAN (R 4.3.0)
    bitops          1.0-7      2021-04-24 [2] CRAN (R 4.3.0)
    bold            1.3.0      2023-05-02 [1] CRAN (R 4.3.0)
    brio            1.1.3      2021-11-30 [2] CRAN (R 4.3.0)
    cachem          1.0.8      2023-05-01 [2] CRAN (R 4.3.0)
    callr           3.7.3      2022-11-02 [2] CRAN (R 4.3.0)
    class           7.3-21     2023-01-23 [2] CRAN (R 4.3.0)
    classInt        0.4-9      2023-02-28 [2] CRAN (R 4.3.0)
    cli             3.6.1      2023-03-23 [2] CRAN (R 4.3.0)
    codemeta        0.1.1      2021-12-22 [1] CRAN (R 4.3.0)
    codetools       0.2-19     2023-02-01 [2] CRAN (R 4.3.0)
    colorspace      2.1-0      2023-01-23 [2] CRAN (R 4.3.0)
    conditionz      0.1.0      2019-04-24 [1] CRAN (R 4.3.0)
    countrycode     1.4.0      2022-05-04 [2] CRAN (R 4.3.0)
    crayon          1.5.2      2022-09-29 [2] CRAN (R 4.3.0)
    crosstalk       1.2.0      2021-11-04 [2] CRAN (R 4.3.0)
    crul            1.4.0      2023-05-17 [1] CRAN (R 4.3.0)
    curl            5.1.0      2023-10-02 [1] CRAN (R 4.3.1)
    cyclocomp       1.1.1      2023-08-30 [1] CRAN (R 4.3.0)
    data.table      1.14.8     2023-02-17 [2] CRAN (R 4.3.0)
    DBI             1.1.3      2022-06-18 [2] CRAN (R 4.3.0)
    desc            1.4.2      2022-09-08 [2] CRAN (R 4.3.0)
    devtools        2.4.5      2022-10-11 [2] CRAN (R 4.3.0)
    dichromat       2.0-0.1    2022-05-02 [1] CRAN (R 4.3.0)
    digest          0.6.33     2023-07-07 [1] CRAN (R 4.3.0)
    dlstats         0.1.7      2023-05-24 [1] CRAN (R 4.3.0)
    dotCall64       1.0-2      2022-10-03 [1] CRAN (R 4.3.0)
    downlit         0.4.3      2023-06-29 [1] CRAN (R 4.3.0)
    dplyr           1.1.3      2023-09-03 [1] CRAN (R 4.3.0)
    dtplyr          1.3.1      2023-03-22 [1] CRAN (R 4.3.0)
    e1071           1.7-13     2023-02-01 [2] CRAN (R 4.3.0)
    ellipsis        0.3.2      2021-04-29 [2] CRAN (R 4.3.0)
    evaluate        0.23       2023-11-01 [1] CRAN (R 4.3.1)
    extrafont       0.19       2023-01-18 [1] CRAN (R 4.3.0)
    extrafontdb     1.0        2012-06-11 [1] CRAN (R 4.3.0)
    fansi           1.0.5      2023-10-08 [1] CRAN (R 4.3.1)
    farver          2.1.1      2022-07-06 [2] CRAN (R 4.3.0)
    fastmap         1.1.1      2023-02-24 [2] CRAN (R 4.3.0)
    fields          14.1       2022-08-12 [1] CRAN (R 4.3.0)
    foreach         1.5.2      2022-02-02 [1] CRAN (R 4.3.0)
    foreign         0.8-84     2022-12-06 [2] CRAN (R 4.3.0)
 VP fs              1.6.2      2023-07-20 [2] CRAN (R 4.3.0) (on disk 1.6.3)
    gdalUtilities   1.2.4      2023-03-21 [1] CRAN (R 4.3.0)
    generics        0.1.3      2022-07-05 [2] CRAN (R 4.3.0)
    geodata         0.5-8      2023-04-14 [1] CRAN (R 4.3.0)
    geojsonsf       2.0.3      2022-05-30 [1] CRAN (R 4.3.0)
    ggforce         0.4.1      2022-10-04 [1] CRAN (R 4.3.0)
    ggplot2         3.4.2      2023-04-03 [2] CRAN (R 4.3.0)
    glue            1.6.2      2022-02-24 [2] CRAN (R 4.3.0)
    gridExtra       2.3        2017-09-09 [2] CRAN (R 4.3.0)
    gtable          0.3.3      2023-03-21 [2] CRAN (R 4.3.0)
    hms             1.1.3      2023-03-21 [2] CRAN (R 4.3.0)
    htmltools       0.5.7      2023-11-03 [1] CRAN (R 4.3.1)
    htmlwidgets     1.6.2      2023-03-17 [2] CRAN (R 4.3.0)
    httpcode        0.3.0      2020-04-10 [2] CRAN (R 4.3.0)
    httpuv          1.6.12     2023-10-23 [1] CRAN (R 4.3.1)
    httr            1.4.7      2023-08-15 [1] CRAN (R 4.3.0)
    httr2           0.2.2      2022-09-25 [2] CRAN (R 4.3.0)
    iterators       1.0.14     2022-02-05 [1] CRAN (R 4.3.0)
    jqr             1.2.3      2022-03-10 [1] CRAN (R 4.3.0)
    jsonlite        1.8.7      2023-06-29 [1] CRAN (R 4.3.0)
    KernSmooth      2.23-20    2021-05-03 [2] CRAN (R 4.3.0)
    keyring         1.3.1      2022-10-27 [1] CRAN (R 4.3.0)
    knitr           1.45       2023-10-30 [1] CRAN (R 4.3.1)
    later           1.3.1      2023-05-02 [2] CRAN (R 4.3.0)
    lattice         0.21-8     2023-04-05 [2] CRAN (R 4.3.0)
    lazyeval        0.2.2      2019-03-15 [2] CRAN (R 4.3.0)
    leafem          0.2.0      2022-04-16 [1] CRAN (R 4.3.0)
    leaflet         2.1.2      2023-03-10 [2] CRAN (R 4.3.0)
    leafsync        0.1.0      2019-03-05 [1] CRAN (R 4.3.0)
    lifecycle       1.0.4      2023-11-07 [1] CRAN (R 4.3.1)
    lintr           3.1.1      2023-11-07 [1] CRAN (R 4.3.1)
    lubridate       1.9.2      2023-02-10 [1] CRAN (R 4.3.0)
    lwgeom          0.2-13     2023-05-22 [1] CRAN (R 4.3.0)
    magrittr        2.0.3      2022-03-30 [2] CRAN (R 4.3.0)
    maps            3.4.1      2022-10-30 [1] CRAN (R 4.3.0)
    maptools        1.1-7      2023-05-29 [1] CRAN (R 4.3.0)
    MASS            7.3-58.4   2023-03-07 [2] CRAN (R 4.3.0)
    memoise         2.0.1      2021-11-26 [2] CRAN (R 4.3.0)
    mime            0.12       2021-09-28 [2] CRAN (R 4.3.0)
    miniUI          0.1.1.1    2018-05-18 [2] CRAN (R 4.3.0)
    MODIStsp        2.0.10     2023-06-12 [1] CRAN (R 4.3.0)
    munsell         0.5.0      2018-06-12 [2] CRAN (R 4.3.0)
    nlme            3.1-162    2023-01-31 [2] CRAN (R 4.3.0)
    oai             0.4.0      2022-11-10 [2] CRAN (R 4.3.0)
    pillar          1.9.0      2023-03-22 [2] CRAN (R 4.3.0)
    pkgbuild        1.4.2      2023-06-26 [1] CRAN (R 4.3.0)
    pkgconfig       2.0.3      2019-09-22 [2] CRAN (R 4.3.0)
    pkgdown         2.0.7      2022-12-14 [1] CRAN (R 4.3.0)
    pkgload         1.3.3      2023-09-22 [1] CRAN (R 4.3.1)
    plyr            1.8.9      2023-10-02 [1] CRAN (R 4.3.1)
    png             0.1-8      2022-11-29 [2] CRAN (R 4.3.0)
    polyclip        1.10-4     2022-10-20 [1] CRAN (R 4.3.0)
    prettyunits     1.2.0      2023-09-24 [1] CRAN (R 4.3.1)
    processx        3.8.2      2023-06-30 [1] CRAN (R 4.3.0)
    profvis         0.3.8      2023-05-02 [2] CRAN (R 4.3.0)
    promises        1.2.1      2023-08-10 [1] CRAN (R 4.3.0)
    proxy           0.4-27     2022-06-09 [2] CRAN (R 4.3.0)
    ps              1.7.5      2023-04-18 [2] CRAN (R 4.3.0)
    purrr           1.0.2      2023-08-10 [1] CRAN (R 4.3.0)
    qrcode          0.2.1      2022-12-18 [1] CRAN (R 4.3.0)
    R6              2.5.1      2021-08-19 [2] CRAN (R 4.3.0)
    rappdirs        0.3.3      2021-01-31 [2] CRAN (R 4.3.0)
    raster          3.6-20     2023-03-06 [2] CRAN (R 4.3.0)
    rbibutils       2.2.13     2023-01-13 [1] CRAN (R 4.3.0)
    RColorBrewer    1.1-3      2022-04-03 [2] CRAN (R 4.3.0)
    Rcpp            1.0.11     2023-07-06 [1] CRAN (R 4.3.0)
    RCurl           1.98-1.12  2023-03-27 [2] CRAN (R 4.3.0)
    rdflib          0.2.7      2023-09-16 [1] CRAN (R 4.3.0)
    Rdpack          2.4        2022-07-20 [1] CRAN (R 4.3.0)
    readr           2.1.4      2023-02-10 [2] CRAN (R 4.3.0)
    rebird          1.3.0      2021-09-20 [1] CRAN (R 4.3.0)
    redland         1.0.17-17  2023-05-23 [1] CRAN (R 4.3.0)
 VP ReLTER        * 2.2.0      2023-10-13 [?] load_all() (on disk 2.1.2)
    remotes         2.4.2      2021-11-30 [2] CRAN (R 4.3.0)
    rex             1.2.1      2021-11-26 [1] CRAN (R 4.3.0)
    rgbif           3.7.7      2023-04-03 [2] CRAN (R 4.3.0)
    ridigbio        0.3.6      2022-08-22 [1] CRAN (R 4.3.0)
    rlang           1.1.2      2023-11-04 [1] CRAN (R 4.3.1)
    rmarkdown       2.25       2023-09-18 [1] CRAN (R 4.3.1)
    rnaturalearth   0.3.2      2023-01-23 [2] CRAN (R 4.3.0)
    rosm            0.2.6      2022-06-09 [1] CRAN (R 4.3.0)
    rotemplate      2.0.0      2023-11-29 [1] Github (ropensci-org/rotemplate@4644c12)
    roxygen2        7.2.3      2022-12-08 [2] CRAN (R 4.3.0)
    rprojroot       2.0.4      2023-11-05 [1] CRAN (R 4.3.1)
    rstudioapi      0.15.0     2023-07-07 [1] CRAN (R 4.3.0)
    Rttf2pt1        1.3.12     2023-01-22 [1] CRAN (R 4.3.0)
    rvertnet        0.8.2      2021-05-13 [1] CRAN (R 4.3.0)
    rworldmap       1.3-6      2016-02-03 [1] CRAN (R 4.3.0)
    s2              1.1.4      2023-05-17 [1] CRAN (R 4.3.0)
    scales          1.2.1      2022-08-20 [2] CRAN (R 4.3.0)
    sessioninfo     1.2.2      2021-12-06 [2] CRAN (R 4.3.0)
    sf              1.0-14     2023-07-11 [1] CRAN (R 4.3.0)
    shiny           1.7.4.1    2023-07-06 [1] CRAN (R 4.3.0)
    sp              1.6-0      2023-01-19 [2] CRAN (R 4.3.0)
    spam            2.9-1      2022-08-07 [1] CRAN (R 4.3.0)
    spocc           1.2.2      2023-03-23 [1] CRAN (R 4.3.0)
    stars           0.6-1      2023-04-06 [1] CRAN (R 4.3.0)
    stringi         1.8.2      2023-11-23 [1] CRAN (R 4.3.1)
    stringr         1.5.1      2023-11-14 [1] CRAN (R 4.3.1)
    taxize          0.9.100    2022-04-22 [1] CRAN (R 4.3.0)
    terra           1.7-29     2023-04-22 [2] CRAN (R 4.3.0)
    testthat      * 3.1.8      2023-05-04 [2] CRAN (R 4.3.0)
    tibble          3.2.1      2023-03-20 [2] CRAN (R 4.3.0)
    tidyr           1.3.0      2023-01-24 [2] CRAN (R 4.3.0)
    tidyselect      1.2.0      2022-10-10 [2] CRAN (R 4.3.0)
    timechange      0.2.0      2023-01-11 [1] CRAN (R 4.3.0)
    tmap            3.3-3      2022-03-02 [1] CRAN (R 4.3.0)
    tmaptools       3.1-1      2021-01-19 [1] CRAN (R 4.3.0)
    tweenr          2.0.2      2022-09-06 [1] CRAN (R 4.3.0)
    tzdb            0.4.0      2023-05-12 [1] CRAN (R 4.3.0)
    units           0.8-3      2023-08-10 [1] CRAN (R 4.3.0)
    urlchecker      1.0.1      2021-11-30 [2] CRAN (R 4.3.0)
    usethis         2.1.6      2022-05-25 [2] CRAN (R 4.3.0)
    utf8            1.2.4      2023-10-22 [1] CRAN (R 4.3.1)
    uuid            1.1-0      2022-04-19 [2] CRAN (R 4.3.0)
    vctrs           0.6.4      2023-10-12 [1] CRAN (R 4.3.1)
    viridis         0.6.4      2023-07-22 [1] CRAN (R 4.3.0)
    viridisLite     0.4.2      2023-05-02 [2] CRAN (R 4.3.0)
    vroom           1.6.4      2023-10-02 [1] CRAN (R 4.3.1)
    waffle          0.7.0      2017-01-07 [1] CRAN (R 4.3.0)
    webshot         0.5.5      2023-06-26 [1] CRAN (R 4.3.0)
    whisker         0.4.1      2022-12-05 [2] CRAN (R 4.3.0)
    withr           2.5.2      2023-10-30 [1] CRAN (R 4.3.1)
    wk              0.7.3      2023-05-06 [2] CRAN (R 4.3.0)
    worrms          0.4.3      2023-06-20 [1] CRAN (R 4.3.0)
    xfun            0.41       2023-11-01 [1] CRAN (R 4.3.1)
    XML             3.99-0.15  2023-11-02 [1] CRAN (R 4.3.1)
    xml2            1.3.5.9000 2023-11-29 [1] Github (r-lib/xml2@b9f65ba)
    xslt            1.4.4      2023-02-21 [1] CRAN (R 4.3.0)
    xtable          1.8-4      2019-04-21 [2] CRAN (R 4.3.0)
    xts             0.13.1     2023-04-16 [1] CRAN (R 4.3.0)
    yaml            2.3.7      2023-01-23 [2] CRAN (R 4.3.0)
    zen4R           0.9.9000   2023-11-03 [1] Github (eblondel/zen4R@f91c899)
    zip             2.3.0      2023-04-17 [2] CRAN (R 4.3.0)
    zoo             1.8-12     2023-04-13 [1] CRAN (R 4.3.0)

 [1] /Users/alessandrooggioni/Library/R/arm64/4.3/library
 [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

 V ── Loaded and on-disk version mismatch.
 P ── Loaded and on-disk path mismatch.

──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
@maelle
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maelle commented Nov 30, 2023

is it correct that I should use the dev branch of ReLTER?

@maelle
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maelle commented Nov 30, 2023

I can reproduce the error with the dev branch and the dev version of pkgdown 👀

@oggioniale
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is it correct that I should use the dev branch of ReLTER?

yes it is correct

@oggioniale
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I can reproduce the error with the dev branch and the dev version of pkgdown 👀

for the pkgdown I use v2.0.7 and not the dev one

@maelle
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maelle commented Nov 30, 2023

thanks to @jonthegeek I see a package with a similar error on CRAN https://cran.r-project.org/web/checks/check_results_cwbtools.html

When is zen4R run in ReLTER exactly? At loading?

Does PolMine/cwbtools#50 ring any bell?

@maelle
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maelle commented Dec 1, 2023

I tried running the build_home() function step by step from pkgdown source and it worked with no message. Then I ran it at once and it also worked with no message. I only see the librdf errors if I run the function from ReLTER.

# from ReLTER folder, errors
pkgdown::build_home()

# from another folder, no error
pkgdown::build_home("../ReLTER")

🤯

@maelle
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maelle commented Dec 1, 2023

But by reverting the idea, loading the pkgdown function from the ReLTER folder, I see the error comes from render_page(). I'll continue investigating.

@maelle
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maelle commented Dec 1, 2023

The error is at xml2::read_html(rendered, encoding = "UTF-8")

@maelle
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maelle commented Dec 1, 2023

the problem comes from having nested p in <p><p>Developed by Alessandro Oggioni, Micha Silver, Paolo Tagliolato, Luigi Ranghetti.</p></p>

@maelle

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@maelle
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maelle commented Dec 1, 2023

Closing as it's not a rotemplate bug. 😸

@maelle maelle closed this as completed Dec 1, 2023
@maelle
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maelle commented Dec 1, 2023

wait maybe it wasn't even the navbar? I'm a bit lost.

@maelle maelle mentioned this issue Dec 1, 2023
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@maelle
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maelle commented Dec 1, 2023

still not sure what the issue is!

r-lib/pkgdown#2381

r-lib/xml2#427

@oggioniale
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wait maybe it wasn't even the navbar? I'm a bit lost.

it isn't because I change the _pkgdown.yaml file like this:

navbar:
  structure:
    left: [reference,articles, news]
    right: [github]

and the librdf error reappears.

@maelle
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maelle commented Dec 1, 2023

yes I noticed that. Maybe I'll hear more from the two aforementioned issues I opened elsewhere. It's really a mystery. Now if the examples and vignettes are fixed, doesn't the website build ok despite the librdf errors?

@ablaette
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You might want to check whether the HTML is valid (can be parsed as XML). After struggling a while with a warnings I see when parsing a website I retrieve from Zenodo, I realized that the same warnings are issued, when I safe the page locally, and run the xmllint command line tool on it.

When I manually edited the html, I successively got rid of the warnings. So there is an invalidity of the HTML document, and the HTML should be changed.

See: PolMine/cwbtools#70

@maelle
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maelle commented May 3, 2024

relevant issue: r-lib/pkgdown#2369

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@oggioniale @ablaette @maelle