mzR requires regular updates of the embedded pwiz and boost libraries.
Theoretically, both could simply be downloaded from their respective
websites and placed under the mzR/src directory. However, the official
downloads contain far more files than required for mzR, and to avoid
massive downloads, only the required files are shipped as part of mzR.
For boost, delete the existing version of boost from mzR/src/boost,
download the full distribution, e.g. boost_1_58_0.tar.gz
and untar into mzR/src/boost. Compile locally with R CMD INSTALL mzR
to make sure that everything works. To detect the minimal set of files,
strace -e open -f R CMD INSTALL .. 2>&1 | grep 'boost/[^=]* = [0-9]' | grep -v boost_aux | cut -d \" -f 2 2>&1 | sort | uniq >/tmp/boost-includes.log
This command logs all access to files under mzR/src/boost.
Then the files can be extracted from the full boost tree:
tar cf - $(sed -e 's/\.o/.cpp/g' /tmp/boost-includes.log) | tar -C newboost -xvf -