Prepare for CRAN release

[zkamvar]

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[zkamvar]

I have attempted to verify this works by using Docker, but I am having trouble installing dartR.base:

> install.packages("dartR.base")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘poisbinom’, ‘SNPassoc’

trying URL 'http://cloud.r-project.org/src/contrib/poisbinom_1.0.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/SNPassoc_2.1-2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/dartR.base_0.98.tar.gz'
* installing *source* package ‘poisbinom’ ...
** this is package ‘poisbinom’ version ‘1.0.1’
** package ‘poisbinom’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Debian 14.2.0-16) 14.2.0’
using C++ compiler: ‘g++ (Debian 14.2.0-16) 14.2.0’
g++ -fsanitize=undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++17 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -fsanitize=undefined -fno-omit-frame-pointer -std=gnu11 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
g++ -fsanitize=undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++17 -I"/usr/local/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c poisbinom.cpp -o poisbinom.o
poisbinom.cpp:3:10: fatal error: fftw3.h: No such file or directory
    3 | #include <fftw3.h>
      |          ^~~~~~~~~
compilation terminated.
make: *** [/usr/local/lib/R/etc/Makeconf:210: poisbinom.o] Error 1
ERROR: compilation failed for package ‘poisbinom’
* removing ‘/usr/local/lib/R/site-library/poisbinom’
ERROR: dependency ‘poisbinom’ is not available for package ‘SNPassoc’
Perhaps try a variation of:
install.packages('poisbinom')
* removing ‘/usr/local/lib/R/site-library/SNPassoc’
ERROR: dependency ‘SNPassoc’ is not available for package ‘dartR.base’
Perhaps try a variation of:
install.packages('SNPassoc')
* removing ‘/usr/local/lib/R/site-library/dartR.base’

The downloaded source packages are in
	‘/tmp/Rtmp2um7Lm/downloaded_packages’
Warning messages:
1: In install.packages("dartR.base") :
  installation of package ‘poisbinom’ had non-zero exit status
2: In install.packages("dartR.base") :
  installation of package ‘SNPassoc’ had non-zero exit status
3: In install.packages("dartR.base") :
  installation of package ‘dartR.base’ had non-zero exit status

This is the contents of the dockerfile I'm working with (which is modified from the one in this repository). Note that I know that I can use install2.r to speed up installation and I will likely do that on my next iteration, but for now, I am done for the night.

FROM rocker/r-devel-san

MAINTAINER Thibaut Jombart <[email protected]>

RUN apt-get update && apt-get upgrade -y
RUN apt-get install -y libcurl4-openssl-dev libssl-dev libfontconfig1-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev gdal-bin proj-bin libgdal-dev libproj-dev libgmp3-dev jags

## add guest user

RUN adduser --disabled-password --gecos "" guest
RUN usermod -a -G users guest && usermod -a -G staff guest
RUN chmod a+rw /usr/local/lib/R/site-library -R



## install CRAN packages

# RUN echo 'options(download.file.method = "libcurl", repos = c(CRAN = "https://cran.ma.imperial.ac.uk"))' > ~/.Rprofile

RUN r -e "install.packages('devtools')" \
 && r -e "install.packages('adegenet', dependencies = TRUE)" \
 && r -e 'install.packages("BiocManager")' \
 && r -e 'BiocManager::install("SNPRelate")' \
 && r -e 'install.packages("dartR.base")'


## clone repos to get sources
RUN apt-get install -y git

RUN su guest
RUN mkdir ~/dev
WORKDIR /home/guest/dev

RUN git clone https://github.com/thibautjombart/adegenet

WORKDIR /home/guest/
CMD Rscript -e 'library(dartR.base); gl.pcoa(testset.gl)'