Closed craig-willis closed 2 years ago
Thank you. I've rewritten quite a lot of the README.Rmd file to address both this and to make the style of the README more formal.
Maybe you are aware of if already but I found pak::pkg_system_requirements()
to be useful for this and I have signposted people to it for more unusual Linux distributions.
I've added a section on developing and running the automated tests
Updated branch: joss-fixes-0.2.4.9000 (and main)
staplr
for pdftools
which has changed the system requirements.I ran into a very minor error during the pkgdown::build_site()
noted below, but otherwise everything looks great.
For reference, here are my steps to confirm dtrackr installation on Ubuntu 20.04 via Docker. I tried to clarify which dependencies belong to each step, if useful.
1. Install r-base
docker run -it ubuntu:focal bash
apt update
# Required to install r-base
apt install -y gnupg software-properties-common
# Install r-base
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
apt update
apt install -y r-base
echo "TZ=$( cat /etc/timezone )" >> /etc/R/Renviron.site
2. Install tidyverse
apt install libcurl4-openssl-dev libssl-dev libxml2-dev
R
> install.packages('tidyverse')
3. Install dtrackr from CRAN
apt install librsvg2-dev libnode-dev
R
> install.packages('dtrackr')
> <Run basic usage example>
> remove.packages('dtrackr')
4. Install dtracker via devtools
apt install libharfbuzz-dev libfribidi-dev libfreetype6-dev libtiff-dev libpoppler-cpp-dev
R
> install.packages("devtools")
> devtools::install_github("terminological/dtrackr")
> <Run basic usage example>
> remove.packages('dtrackr')
5. Install dtrackr from source
apt-get install git
# Clone repo
git clone https://github.com/terminological/dtrackr
cd dtrackr
R
> install.packages(".", repos=NULL, type="source")
6. Run tests
> install.packages('pak')
> devtools::load_all()
> pak::local_system_requirements("ubuntu","20.04")
> install.packages(c("here","tidyverse","devtools","testthat","pkgdown"))
> devtools::run_examples()
> devtools::test()
...
== Results ======================================================================
Duration: 174.1 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 144 ]
Build site
apt install make pandoc imagemagick libmagick++-dev \
gsfonts default-jdk zlib1g-dev libfontconfig1-dev \
libjpeg-dev libpng-dev libgit2-dev
> pkgdown::build_site()
...
Error in render_rmarkdown(pkg, input = input, output = output_file, output_format = format, :
Failed to render RMarkdown
Caused by error:
! error in callr subprocess
Caused by error:
! pandoc document conversion failed with error 83
In addition: Warning message:
Missing images in 'README.md': 'reference/figures/README-flowchart.png?raw=true'
i pkgdown can only use images in 'man/figures' and 'vignettes'
Install covr dependencies
apt install pandoc-citeproc
> install.packages('covr')
> covr::package_coverage(type="all", quiet = FALSE)
...
dtrackr Coverage: 83.60%
R/dot.R: 78.12%
R/dtrackr.R: 84.08%
Revised branch: joss-fixes-0.2.4.9000
Looks great (edit see above comment for details).
Review issue: https://github.com/openjournals/joss-reviews/issues/4707 Branch reviewed: release-0.2.4
Problem: The JOSS guidelines require clear Installation instructions. I attempted to install
dtrackr
on a fresh Ubuntu 20.04 (via Docker) with R 4.2.1 and encountered several errors due to missing OS packages. These could be inferred from the required R packages, but it would be helpful to have a complete list in the installation instructions. Additional packages and OS dependencies were required to run the automated tests and could also be clearer.What I had to install:
For automated tests:
Consider adding a comprehensive list of dependencies as well as supported OS and R versions to the "Installing" section of the readme.