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NOTES.md

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To install using devtools

roxygen2::roxygenise("..")
devtools::install(".", build_vignettes=TRUE)

The build_vignettes argument is needed because the Qhull docs now have to be installed in inst/doc using the .install_extras file in the vignettes directory.

To do a reverse dependency check

Github actions method

  1. Browse to the Actions page on Github and then select Reverse dependency check. Alternatively go directly to this URL: https://github.com/davidcsterratt/geometry/actions/workflows/recheck.yml
  2. Click on Run Workflow and wait about an hour for results
  3. Once done, click on the top Reverse dependency check row and then Show results.
  4. Examine the Get results section, which presents some summary level information of the number of packages with Warning and Errors.
  5. You can also download the old and new package logs, unzip them into to two separate directories, and diff them using 
    diff -ru -x '*.Rout' -x '*manual.log' -x 'Rdlatex.log' newpkg-checklogs-pre newpkg-checklogs-post/  |grep Status

Revdepcheck method

Install and use the revdepcheck package as follows:

revdepcheck::revdep_check("geometry/pkg", num_workers=6)

CRAN manual method

  1. Make sure relevant system packages are install. On Debian/Ubuntu Linux: 
    sudo apt install libgmp-dev cmake libudunits2-dev libgdal-dev libgsl-dev libglpk-dev libmagick++-dev libpoppler-cpp-dev
  2. Build the package using R CMD check.
  3. Put the constructed .tar.gz file in a directory on its own
  4. Open R in this directory, and run 
    tools::check_packages_in_dir(reverse = list(), dir='revdep-rtools', pfiles='geometry_0.4.8.tar.gz', clean=FALSE)

To spell check

devtools::spell_check("pkg")

Update any words to ignore in pkg/inst/WORDLIST.

To recreate registration skeleton

If changing any arguements to C or C++ functions:

tools::package_native_routine_registration_skeleton("geometry/pkg")

To update links in qhull docs

The QHull html docs are copied from the Qhull source tree (qhull/html) to vignettes/qhull/html. To satisfy the R checks, files have to be renamed from *.htm to *.html, and the links have to be updated too. In order to do this, once all doc files have been copied into pkg/inst/doc/html, the following bash commands work:

for f in *.htm; do mv ${f} ${f}l ; done
for f in *.html; do for g in *.html ; do echo  perl -p -i -e \'s/`basename ${f} .html`\\.htm/${f}/g\;\' $g ; done ; done > commands
. commands
rm commands

To check for protection errors with rchk

  1. Install rchk using the automated installation method https://github.com/kalibera/rchk#automated-installation

  2. Build R as described at https://github.com/kalibera/rchk#testing-the-installation

  3. Install current geometry and dependencies

. /opt/rchk/scripts/config.inc
. /opt/rchk/scripts/cmpconfig.inc
cd ~/trunk
echo 'install.packages(c("geometry", "Rcpp", "lpSolve", "RcppProgress"), repos="http://cloud.r-project.org")' | ./bin/R --slave
  1. Install github version of geometry and check
cd ~
git clone https://github.com/davidcsterratt/geometry
cd trunk
echo 'install.packages("../geometry_0.4.0.tar.gz")' | ./bin/R --slave
/opt/rchk/scripts/check_package.sh
cat packages/lib/geometry/libs/geometry.so.*check
  1. When a new change to the github version made, recheck:
cd ~/geometry
git pull
cd
./trunk/bin/R CMD build geometry/pkg
cd ~/trunk
echo 'install.packages("../geometry_0.4.0.tar.gz")' | ./bin/R --slave
/opt/rchk/scripts/check_package.sh geometry
cat packages/lib/geometry/libs/geometry.so.*check
  1. After having logged out neceesary to do Step 3 again.