Installing dropEst, R issues

Users are recommended to install dropEst with CMake, which will inform users of missing dependencies. Common issues are described in Troubleshooting

The command for installing dropEst is:

git clone https://github.com/hms-dbmi/dropEst.git
cd dropEst
cmake . 
## check if there are errors
make

Dependencies are described here:

• Boost >= 1.54
• BamTools library >= 2.5.0
• Zlib (was tested on 1.2.11 version)
• Bzip2 (was tested on 1.0.5 version)
• R >= 3.2.2 with packages:
  • Rcpp
  • RcppEigen
  • RInside
  • Matrix
• Compiler with c++11 support (was tested with gcc >= 4.8.5 and CLang 3.9.1)
• CMake >= 3.0

NOTE: For bamtools, some linux distributions have separate packages for the library and the executable (e.g. on Ubuntu you need libbamtools-dev, but not bamtools) or you can build it locally and then specify the location of the build when running cmake (e.g. cmake -D BAMTOOLS_ROOT=/home/username/bamtools).

Note that there are additional checks for R:

(1) Users must set the variables R_ROOT and R_PACKAGES. To find these, try the following commands with your R session:

> .libPaths()
## [1] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library"
> R.home()
## [1] "/Library/Frameworks/R.framework/Resources"

The first path .libPaths() should be the path for the variable R_PACKAGES, and the second should be R_ROOT.

Set these libraries as follows:

R_ROOT=/Library/Frameworks/R.framework/Resources
R_PACKAGES=/Library/Frameworks/R.framework/Versions/4.0/Resources/library

(2) R must be configured and built with --enable-R-shlib:

./configure --prefix=/opt/R/3.2.3 --enable-R-shlib
make
make install

This will create the shared library libR.so. If this doesn't exist, users must install R with --enable-R-shlib.