Hello everybody,

I am trying to install the package flowDensity when building a docker container using the latest release_core2. I receive the following error:

ERROR: dependencies ‘rgeos’, ‘flowWorkspace’ are not available for package ‘flowDensity’

I could fix the first one by adding apt-get install libgeos-dev. However, the second one is more tricky. It comes down to the package RProtoBufLib, which is a dependency for cytolib and hence for flowWorkspace. I receive the following error when installing RProtoBufLib:

config.status: error: cannot find input file: `config.h.in'
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /tmp/Rtmpro4BMN/R.INSTALL65e11754ab1d/RProtoBufLib/src/protobuf-2.6.0/missing aclocal-1.14 -I m4
/tmp/Rtmpro4BMN/R.INSTALL65e11754ab1d/RProtoBufLib/src/protobuf-2.6.0/missing: line 81: aclocal-1.14: command not found
WARNING: 'aclocal-1.14' is missing on your system.
         You should only need it if you modified 'acinclude.m4' or
         'configure.ac' or m4 files included by 'configure.ac'.
         The 'aclocal' program is part of the GNU Automake package:
         <http://www.gnu.org/software/automake>
         It also requires GNU Autoconf, GNU m4 and Perl in order to run:
         <http://www.gnu.org/software/autoconf>
         <http://www.gnu.org/software/m4/>
         <http://www.perl.org/>
make: *** [aclocal.m4] Error 127
Makefile:407: recipe for target 'aclocal.m4' failed

I found some posts on google about how to edit the PATH on Linux in order to fix this, but I have no idea how to go about this when building a docker container. Any suggestions are welcome. Thanks!

Try apt-get install dh-autoreconf this should install the correct versions of automake that is needed. Once this was run I was able to biocLite("RProtoBufLib")