Build failing

[nacnudus]

Packrat fails to install Rcpp.

error: '::Rf_pythag' has not been declared

It was removed from R on 15 March 2018 .

It was removed from Rcpp on 28 February 2018, released in version 0.12.16 on 2018-03-08.

2018-02-28  Dirk Eddelbuettel  

        * inst/include/Rcpp/Rmath.h (R): Rf_pythag has been remove in R 2.14.0
        so comment-out the R::pythag wrapper (per request of Brian Ripley)

Packrat attempts to install Rcpp version 0.12.12 released on 2017-07-13.

rap_companion/packrat/packrat.lock

Lines 21 to 24 in da70797

	Package: Rcpp
	Source: CRAN
	Version: 0.12.12
	Hash: 8b3d5ebb9a9a4ab5c86b3a81b0cfb774

.

If the build succeeds with the latest versions of Rcpp then that will be the fix.

[nacnudus]

#88 fixes the installation of Rcpp and reveals the next problem.

processing file: 14-final.Rmd
  |.................................................................| 100%
  ordinary text without R code
output file: 14-final.knit.md
/usr/bin/pandoc +RTS -K512m -RTS rap_companion.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output rap_companion.html --smart --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/travis/build/ukgovdatascience/rap_companion/packrat/lib/x86_64-pc-linux-gnu/3.5.1/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css style.css --include-in-header /tmp/RtmpL5hg35/rmarkdown-str4b3cd99d56d.html --mathjax --include-in-header google_analytics.html 
Error in get0(oNam, envir = ns) : 
  lazy-load database '/home/travis/build/ukgovdatascience/rap_companion/packrat/lib/x86_64-pc-linux-gnu/3.5.1/stringr/R/stringr.rdb' is corrupt
Calls: <Anonymous> ... process_images -> process_html_res -> :: -> getExportedValue -> get0
In addition: Warning message:
In get0(oNam, envir = ns) : internal error -3 in R_decompress1
Please delete rap_companion.md after you finish debugging the error.
Execution halted
The command "./_build.sh" exited with 1.

While running /_build.sh locally I noticed that a chunk installs a package.

rap_companion/04-exemplar.Rmd

Lines 163 to 168 in da70797

	```{r, echo=FALSE}
	devtools::install_github('ukgovdatascience/eesectors')
	library(eesectors)
	```

The installation code devtools::install_github('ukgovdatascience/eesectors') should be in its own chunk with the chunk option eval = FALSE to prevent it (and many big dependencies) being reinstalled. It will already have been installed by packrat.

[nacnudus]

Running /_build.sh locally failed on the 14th chapter due to pandoc's API for smart quotes changing. I remember having that problem before, quite a while ago, so I'll try upgrading pandoc.

processing file: 14-final.Rmd
  |.................................................................| 100%
  ordinary text without R code


output file: 14-final.knit.md

/usr/bin/pandoc +RTS -K512m -RTS rap_companion.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output rap_companion.html --smart --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/nacnudus/gds/datascience/rap/rap_companion/packrat/lib/x86_64-pc-linux-gnu/3.5.2/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css style.css --include-in-header /tmp/Rtmpj8OfpH/rmarkdown-str4efe61809e5f.html --mathjax --include-in-header google_analytics.html 
--smart/-S has been removed.  Use +smart or -smart extension instead.
For example: pandoc -f markdown+smart -t markdown-smart.
Try pandoc --help for more information.
Error: pandoc document conversion failed with error 2
Please delete rap_companion.md after you finish debugging the error.

[nacnudus]

There's no pandoc to upgrade -- pandoc is on the system, not in R -- so I upgraded rmarkdown and its dependencies (knitr etc.) and ended up with object 'tojson' not found. tojson() is in the xfun package, which was up to date, but I gave up at that point and did devtools::update_packages() for all packages, which broke packrat.

Error in !packrat::opts$symlink.system.packages() : invalid argument type

Following the workaround in that issue, I deleted the /packrat/lib and /packrat/src directories, restarted R and packrat bootstrapped itself. Same error. Running packrat::set_opts(symlink.system.packages = TRUE) fixed it. The book builds locally.

[nacnudus]

I reverted 3b0d154 and will deal with local pandoc in a separate issue.