After upgrading to R 3.3.0 and Bioc 3.3, installing the RBGL package
BioC_mirror: http://mirrors.ebi.ac.uk/bioconductor Using Bioconductor 3.3 (BiocInstaller 1.22.1), R 3.3.0 (2016-05-03). Installing package(s) ‘RBGL’ trying URL 'http://mirrors.ebi.ac.uk/bioconductor/packages/3.3/bioc/src/contrib/RBGL_1.48.0.tar.gz' Content type 'application/x-gzip' length 2278218 bytes (2.2 MB) ================================================== downloaded 2.2 MB * installing *source* package ‘RBGL’ ... untarring boost include tree... ** libs clang++ -I/usr/local/Cellar/r/3.3.0/R.framework/Resources/include -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -Irbgl_trimmed_boost_1_49_0 -fPIC -g -O2 -c bbc.cpp -o bbc.o In file included from bbc.cpp:3: In file included from /usr/local/include/boost/graph/bc_clustering.hpp:14: In file included from /usr/local/include/boost/graph/graph_utility.hpp:32: In file included from /usr/local/include/boost/graph/depth_first_search.hpp:27: In file included from /usr/local/include/boost/tti/has_member_function.hpp:15: In file included from /usr/local/include/boost/tti/detail/dmem_fun.hpp:11: In file included from /usr/local/include/boost/function_types/is_member_function_pointer.hpp:14: In file included from /usr/local/include/boost/function_types/components.hpp:44: In file included from /usr/local/include/boost/mpl/remove.hpp:18: /usr/local/include/boost/mpl/remove_if.hpp:55:15: error: expected '(' for function-style cast or type construction > > ~ ^ /usr/local/include/boost/mpl/remove_if.hpp:56:9: error: expected class name > ^ /usr/local/include/boost/mpl/remove_if.hpp:72:15: error: expected '(' for function-style cast or type construction > > ~ ^ /usr/local/include/boost/mpl/remove_if.hpp:73:9: error: expected class name > ^ 4 errors generated. make: *** [bbc.o] Error 1 ERROR: compilation failed for package ‘RBGL’ * removing ‘/usr/local/lib/R/3.3/site-library/RBGL’ The downloaded source packages are in ‘/private/var/folders/_7/hb3h1xr10yz3csf7bdhkm5xx8y1cf0/T/RtmpIV0Juy/downloaded_packages’ Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘RBGL’ had non-zero exit status
This may be related to the report: Install SomaticSignatures (ERROR: compilation failed for package 'RBGL')
Does anyone have an idea how this can be resolved?
R version 3.3.0 (2016-05-03) Platform: x86_64-apple-darwin15.4.0 (64-bit) Running under: OS X 10.11.4 (El Capitan) locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.22.1 loaded via a namespace (and not attached):  tools_3.3.0
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/4.2.1 Apple LLVM version 7.3.0 (clang-703.0.31) Target: x86_64-apple-darwin15.4.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin