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r-lib / pkgdown

Generate static html documentation for an R package
https://pkgdown.r-lib.org/
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Error reading the DESCRIPTION file #451

Closed Robinlovelace closed 6 years ago

Robinlovelace commented 6 years ago

I'm bamboozled at this error message:


> pkgdown::build_site()
Initialising site ------------------------------------------------------------------------------------------------
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/jquery.sticky-kit.min.js'
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/link.svg'
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/pkgdown.css'
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/pkgdown.js'
Building home ----------------------------------------------------------------------------------------------------
Writing '/home/robin/repos/stplanr/docs/authors.html'
Updating README.md
Building article 'index.html'
Error in read.dcf("DESCRIPTION") : cannot open the connection

Any ideas? As the below reprex shows there's seemingly nowt wrong with DESCRPTION from the perspective of read.dcf()...

Robinlovelace commented 6 years ago 
read.dcf("/home/robin/repos/stplanr/DESCRIPTION")
#>      Package   Type      Title                            Version
#> [1,] "stplanr" "Package" "Sustainable Transport Planning" "0.2.1"
#>      Authors@R                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
#> [1,] "c(\nperson(\"Robin\", \"Lovelace\", email = \"rob00x@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5679-6536\")),\nperson(\"Richard\", \"Ellison\", role = c(\"aut\")),\nperson(\"Barry\", \"Rowlingson\", role = c(\"ctb\"), comment = \"Author of overline\"),\nperson(\"Nick\", \"Bearman\", role = c(\"ctb\"), comment = \"Co-author of gclip\"),\nperson(\"Malcolm\", \"Morgan\", role = c(\"ctb\"), comment = \"Co-author of angle_diff\"),\nperson(\"Nikolai\", \"Berkoff\", role = c(\"ctb\"), comment = \"Co-author of line2route\"),\nperson(\"Scott \", \"Chamberlin\", role = c(\"rev\"), comment = \"Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10\")\n)"
#>      Maintainer                         
#> [1,] "Robin Lovelace <rob00x@gmail.com>"
#>      Description                                                                                                                                           
#> [1,] "Functionality and data access tools for transport planning,\nincluding origin-destination analysis, route allocation and modelling travel\npatterns."
#>      License              BugReports                                  
#> [1,] "MIT + file LICENSE" "https://github.com/ropensci/stplanr/issues"
#>      LazyData Depends          
#> [1,] "yes"    "sp,\nR (>= 3.0)"
#>      Imports                                                                                                                                                                                                 
#> [1,] "curl,\nreadr,\ndplyr,\nhttr,\njsonlite,\nstringi,\nstringr,\nlubridate,\nmaptools,\nraster,\nrgdal,\nrgeos,\nopenxlsx,\nmethods,\nR.utils,\ngeosphere,\nRcpp (>= 0.12.1),\nigraph,\nnabor,\nrlang,\nsf"
#>      LinkingTo              Suggests                              
#> [1,] "RcppArmadillo,\nRcpp" "testthat,\nknitr,\nrmarkdown,\ndodgr"
#>      Enhances VignetteBuilder URL                                  
#> [1,] "tmap"   "knitr"         "https://github.com/ropensci/stplanr"
#>      SystemRequirements RoxygenNote
#> [1,] "GNU make"         "6.0.1"
hadley commented 6 years ago

Did you manage to figure this out in the meantime?

If not, can you please point me to the source repo?

Robinlovelace commented 6 years ago

Just tested and am still getting the error, using the same version of pkgdown it looks like this:

> pkgdown::build_site()
Initialising site ---------------------------------------------------------------------------------------------------------------------------------------------------------------
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/jquery.sticky-kit.min.js'
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/link.svg'
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/pkgdown.css'
Copying '/home/robin/R/x86_64-pc-linux-gnu-library/3.4/pkgdown/assets/pkgdown.js'
Building home -------------------------------------------------------------------------------------------------------------------------------------------------------------------
Writing '/home/robin/repos/stplanr/docs/LICENSE.html'
Writing '/home/robin/repos/stplanr/docs/authors.html'
Updating README.md
Building article 'index.html'
Error in read.dcf("DESCRIPTION") : cannot open the connection
Robinlovelace commented 6 years ago

Pointer to the source repo: https://github.com/ropensci/stplanr

hadley commented 6 years ago

I get a couple of different failures, once of which is a pkgdown problem. But when I try and knit that index.Rmd I get:

label: rnet (with options) 
List of 1
 $ warning: logi FALSE

Assertion failed: (!"should never be reached"), function itemsTree, file ../../../../src/geos-3.6.1/src/index/strtree/AbstractSTRtree.cpp, line 373.
hadley commented 6 years ago

I also get an uninformative error message, but it looks like it's a buglet in callr: https://github.com/r-lib/callr/issues/41

Robinlovelace commented 6 years ago

Thanks for the fix. I'm getting a different error now though with the latest version, any ideas?

Error in section_init(pkg, depth = depth) : object 'depth' not found
dblodgett-usgs commented 6 years ago

@hadley -- did you identify what was causing the error :

Assertion failed: (!"should never be reached"), function itemsTree, file ../../../../src/geos-3.6.1/src/index/strtree/AbstractSTRtree.cpp, line 373.

I am getting the exact error when running tests in rstudio but not if I run test_file("...") and this is the only reference to it on google. I can not reproduce this outside the context of a test run...

Thanks for any guidance you can provide!

dblodgett-usgs commented 6 years ago

Stab in the dark uninstall and reinstall of rgeos using: 

install.packages("rgeos", repos="http://R-Forge.R-project.org", type="source")

Seams to have fixed it. Not sure I want to know what was actually wrong!

Robinlovelace commented 6 years ago

Who knows. Pkgdown seems to be working again now though which is great. Thanks all!