After updating Bioconductor to the latest version:

> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.0), R 3.2.2 (2015-08-14).
Old packages: 'flowWorkspace'
Update all/some/none? [a/s/n]: y

I get the following error message:

g++ -I/ifs/apps/apps/R-3.2.2/lib64/R/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -Iboost_serialization -I/usr/local/include -I"/ifs/apps/apps/R-3.2.2/lib64/R/library/Rcpp/include" -I"/ifs/apps/apps/R-3.2.2/lib64/R/library/BH/include"   -fpic  -g -O2  -c GatingHierarchy.cpp -o GatingHierarchy.o
cc1plus: error: unrecognized command line option "-ftemplate-depth=900"
make: *** [GatingHierarchy.o] Error 1
ERROR: compilation failed for package 'flowWorkspace'

Does anybody know why?

Many thanks in advance for your help.

I just pushed the fix yesterday and flowWorkspace 3.16.2 should appear at bioconductor site by the end of today.