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put-in-bioc-git-dir-and-test.sh
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put-in-bioc-git-dir-and-test.sh
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#!/bin/bash
## This places the code to upload to BioC git repo in the right place.
## If passed an additional argument, with the path of an R version, it
## builds and tests.
## Yes, works under eshell.
## I need to clean up first, because otherwise when I remove files in the
## master git repo, they are not necessarily removed in the svn repo
rm ../BioConductor-git/OncoSimulR/vignettes/*
rm ../BioConductor-git/OncoSimulR/tests/*
rm ../BioConductor-git/OncoSimulR/tests/manual/*
rm ../BioConductor-git/OncoSimulR/tests/testthat/*
rm ../BioConductor-git/OncoSimulR/src/*
rm ../BioConductor-git/OncoSimulR/R/*
rm ../BioConductor-git/OncoSimulR/man/*
rm ../BioConductor-git/OncoSimulR/data/*
rm ../BioConductor-git/OncoSimulR/inst/*
rm ../BioConductor-git/OncoSimulR/inst/miscell/*
cp OncoSimulR/vignettes/relfunct.tex ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/preamble.tex ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/relfunct.png ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/custom4.css ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/OncoSimulR.Rmd ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/OncoSimulR.bib ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/gitsetinfo.sty ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/gitinfo.sty ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/gitHeadInfo.gin ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/hurlbut.png ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/hurlbut.pdf ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/Myeloma_interaction.png ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/logo-micin-aei-uefeder.png ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/logo-micin-aei.png ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/vignettes/apa.csl ../BioConductor-git/OncoSimulR/vignettes/.
cp OncoSimulR/src/*.c ../BioConductor-git/OncoSimulR/src/.
cp OncoSimulR/src/*.cpp ../BioConductor-git/OncoSimulR/src/.
cp OncoSimulR/src/*.h ../BioConductor-git/OncoSimulR/src/.
cp OncoSimulR/src/Makevars* ../BioConductor-git/OncoSimulR/src/.
cp OncoSimulR/src/install.libs.R ../BioConductor-git/OncoSimulR/src/.
cp OncoSimulR/src/UnityOncoSimul/* ../BioConductor-git/OncoSimulR/src/UnityOncoSimul/.
cp OncoSimulR/src/FitnessLandscape/* ../BioConductor-git/OncoSimulR/src/FitnessLandscape/.
cp OncoSimulR/src/FitnessLandscape/web/* ../BioConductor-git/OncoSimulR/src/FitnessLandscape/web/.
cp OncoSimulR/R/*.R ../BioConductor-git/OncoSimulR/R/.
cp OncoSimulR/tests/testthat.R ../BioConductor-git/OncoSimulR/tests/.
cp OncoSimulR/tests/testthat/*.R ../BioConductor-git/OncoSimulR/tests/testthat/.
cp OncoSimulR/tests/manual/*.R ../BioConductor-git/OncoSimulR/tests/manual/.
cp OncoSimulR/tests/manual/*.txt ../BioConductor-git/OncoSimulR/tests/manual/.
cp OncoSimulR/tests/manual/user_vars/* ../BioConductor-git/OncoSimulR/tests/manual/user_vars/.
cp OncoSimulR/tests/*.txt ../BioConductor-git/OncoSimulR/tests/.
cp OncoSimulR/man/*.Rd ../BioConductor-git/OncoSimulR/man/.
cp OncoSimulR/inst/README_Unity_compilation.txt ../BioConductor-git/OncoSimulR/inst/.
cp OncoSimulR/inst/NEWS ../BioConductor-git/OncoSimulR/inst/.
cp OncoSimulR/inst/CITATION ../BioConductor-git/OncoSimulR/inst/.
cp OncoSimulR/inst/miscell/example-binom-problems.cpp ../BioConductor-git/OncoSimulR/inst/miscell/.
cp OncoSimulR/inst/miscell/*.R ../BioConductor-git/OncoSimulR/inst/miscell/.
cp OncoSimulR/inst/testdata_fee.RData ../BioConductor-git/OncoSimulR/inst/.
cp OncoSimulR/data/*.RData ../BioConductor-git/OncoSimulR/data/.
cp OncoSimulR/NAMESPACE ../BioConductor-git/OncoSimulR/.
cp OncoSimulR/DESCRIPTION ../BioConductor-git/OncoSimulR/.
cp OncoSimulR/.BBSoptions ../BioConductor-git/OncoSimulR/.
## We always do this, though it should not be necessary
sed -i 's/^};$/}/' ../BioConductor-git/OncoSimulR/src/FitnessLandscape/generalized_chain.c
## should we run the tests?
export R_CHECK_ENVIRON="~/.R/Renviron.bioc" ## see https://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc
if [[ $# == 1 ]]; then
V_R=$1
cd ~/Proyectos/BioConductor-git
V_P=$(cat ./OncoSimulR/DESCRIPTION | grep Version | cut -d' ' -f2)
rm OncoSimulR_$V_P.tar.gz
## As shown in build report from BioC
echo " ***************************************** "
echo " ********* R CMD build vanilla ************** "
echo " "
time $V_R --vanilla CMD build --keep-empty-dirs --no-resave-data OncoSimulR
echo " "
echo " =========== done R CMD build vanilla ========== "
echo " "
## As shown in check report from BioC
echo " *************************************************** "
echo " **** R CMD check vanilla , as in check report **** "
echo ""
time $V_R --vanilla CMD check --no-vignettes --timings OncoSimulR_$V_P.tar.gz
echo " "
echo " ========= done R CMD check vanilla as in check report ======= "
echo " "
## time as explained in https://www.bioconductor.org/developers/package-guidelines/#correctness
echo " ************************************ "
fi
## Check what/if things need adding
cd ~/Proyectos/BioConductor-git/OncoSimulR
git status | less