dev script updates only: CRAN_Release, and added my .bash_aliases and .Rprofile

Author: mattdowle

.dev/.Rprofile

@@ -0,0 +1,14 @@
+# Matt's ~/.Rprofile is a link to this file at ~/GitHub/data.table/.dev/.Rprofile
+
+# options(repos = c(CRAN="http://cran.stat.ucla.edu"))
+# options(repos = c(CRAN=c("http://cran.stat.ucla.edu", "http://cloud.r-project.org")))  # both needed for revdep checks sometimes
+options(repos = c(CRAN="http://cloud.r-project.org"))
+
+options(help_type="html")
+options(error=quote(dump.frames()))
+options(width=200)
+options(digits.secs=3)  # for POSIXct to print milliseconds
+suppressWarnings(RNGversion("3.5.0"))  # so when I create tests in dev there isn't a mismatch when run by cc()
+
+Sys.setenv(PROJ_PATH=path.expand("~/GitHub/data.table"))
+source(paste0(Sys.getenv("PROJ_PATH"),"/.dev/cc.R"))

.dev/.bash_aliases

@@ -0,0 +1,21 @@
+# Matt's ~/.bash_aliases is a link to this file ~/GitHub/data.table/.dev/.bash_aliases
+
+# One off configure meld as difftool:
+# git config --global diff.tool meld
+# git config --global difftool.prompt false
+alias gd='git difftool &> /dev/null'
+alias gdm='git difftool master &> /dev/null'
+
+alias Rdevel='~/build/R-devel/bin/R --vanilla'
+alias Rdevel-strict-gcc='~/build/R-devel-strict-gcc/bin/R --vanilla'
+alias Rdevel-strict-clang='~/build/R-devel-strict-clang/bin/R --vanilla'
+alias Rdevel32='~/build/32bit/R-devel/bin/R --vanilla'
+alias R310='~/build/R-3.1.0/bin/R --vanilla'
+alias revdepsh='cd ~/build/revdeplib/ && export TZ=UTC && export R_LIBS_SITE=none && export R_LIBS=~/build/revdeplib/ && export _R_CHECK_FORCE_SUGGESTS_=false'
+alias revdepr='revdepsh; R_PROFILE_USER=~/GitHub/data.table/.dev/revdep.R ~/build/R-devel/bin/R'
+
+export R_PROFILE_USER='~/.Rprofile'
+# there's a .Rprofile in ~/GitHub/data.table/ so Matt sets R_PROFILE_USER here to always use ~/.Rprofile
+# even when starting R in ~/GitHub/data.table
+# Matt's ~/.Rprofile as a link to ~/GitHub/data.table/.dev/.Rprofile
+

.dev/CRAN_Release.cmd

@@ -304,7 +304,7 @@ cd R-devel  # used for revdep testing: .dev/revdep.R.
 ./configure CFLAGS="-O2 -Wall -pedantic"
 make
 
-# use latest available below `apt cache search gcc-` or `clang-`
+# use latest available below `apt-cache search gcc-` or `clang-`
 cd ../R-devel-strict-clang
 ./configure --without-recommended-packages --disable-byte-compiled-packages --disable-openmp --enable-strict-barrier --disable-long-double CC="clang-8 -fsanitize=undefined,address -fno-sanitize=float-divide-by-zero -fno-omit-frame-pointer"
 make
@@ -479,7 +479,7 @@ sudo apt-get -y install r-base r-base-dev
 sudo apt-get -y build-dep r-base-dev
 sudo apt-get -y build-dep qpdf
 sudo apt-get -y install aptitude
-sudo aptitude build-dep r-cran-rgl   # leads to libglu1-mesa-dev
+sudo aptitude -y build-dep r-cran-rgl   # leads to libglu1-mesa-dev
 sudo apt-get -y build-dep r-cran-rmpi
 sudo apt-get -y build-dep r-cran-cairodevice
 sudo apt-get -y build-dep r-cran-tkrplot
@@ -490,8 +490,7 @@ sudo apt-get -y install libv8-dev
 sudo apt-get -y install gsl-bin libgsl0-dev
 sudo apt-get -y install libgtk2.0-dev netcdf-bin
 sudo apt-get -y install libcanberra-gtk-module
-sudo apt-get -y install git
-sudo apt-get -y install openjdk-8-jdk
+sudo apt-get -y install openjdk-11-jdk   # solves "fatal error: jni.h: No such file or directory"; change 11 to match "java --version"
 sudo apt-get -y install libnetcdf-dev udunits-bin libudunits2-dev
 sudo apt-get -y install tk8.6-dev
 sudo apt-get -y install clustalo  # for package LowMACA
@@ -512,14 +511,16 @@ sudo apt-get -y install libmagick++-dev  # for magick
 sudo apt-get -y install libjq-dev libprotoc-dev libprotobuf-dev and protobuf-compiler   # for protolite
 sudo apt-get -y install python-dev  # for PythonInR
 sudo apt-get -y install gdal-bin libgeos-dev  # for rgdal/raster tested via lidR
-sudo apt-get build-dep r-cran-rsymphony   # for Rsymphony: coinor-libcgl-dev coinor-libclp-dev coinor-libcoinutils-dev coinor-libosi-dev coinor-libsymphony-dev
+sudo apt-get -y build-dep r-cran-rsymphony   # for Rsymphony: coinor-libcgl-dev coinor-libclp-dev coinor-libcoinutils-dev coinor-libosi-dev coinor-libsymphony-dev
 sudo apt-get -y install libtesseract-dev libleptonica-dev tesseract-ocr-eng   # for tesseract
 sudo apt-get -y install libssl-dev libsasl2-dev
 sudo apt-get -y install biber   # for ctsem
 sudo apt-get -y install libopenblas-dev  # for ivmte (+ local R build with default ./configure to pick up shared openblas)
 sudo apt-get -y install libhiredis-dev  # for redux used by nodbi
 sudo apt-get -y install libzmq3-dev   # for rzmq
 sudo apt-get -y install libimage-exiftool-perl   # for camtrapR
+sudo apt-get -y install parallel   # for revdepr.R
+sudo apt-get -y install pandoc-citeproc   # for basecallQC
 sudo R CMD javareconf
 # ENDIF