I am trying to install flowCore package (Bioconductor 3.4) in R 3.3.2 (Ubuntu 14.04 LTS). But I am getting following error. Can anybody suggest some solution thanks.
boost_regex/regex.cpp:195:64: error: use of deleted function ‘std::atomic<_Tp*>::atomic(const std::atomic<_Tp*>&) [with _Tp = void]’
mem_block_cache block_cache = { 0, 0, BOOST_STATIC_MUTEX_INIT, };
^
In file included from /home/nitin/R/x86_64-pc-linux-gnu-library/3.3/BH/include/boost/regex/v4/mem_block_cache.hpp:31:0,
from boost_regex/regex.cpp:44:
/usr/include/c++/4.8/atomic:298:7: error: declared here
atomic(const atomic&) = delete;
^
boost_regex/regex.cpp:195:64: error: use of deleted function ‘std::atomic<_Tp*>::atomic(const std::atomic<_Tp*>&) [with _Tp = void]’
mem_block_cache block_cache = { 0, 0, BOOST_STATIC_MUTEX_INIT, };
^
In file included from /home/nitin/R/x86_64-pc-linux-gnu-library/3.3/BH/include/boost/regex/v4/mem_block_cache.hpp:31:0,
from boost_regex/regex.cpp:44:
/usr/include/c++/4.8/atomic:298:7: error: declared here
atomic(const atomic&) = delete;
^
boost_regex/regex.cpp:195:64: error: could not convert ‘{{{0, 0, 0, 0, 0, 0, 0, {0, 0}}}}’ from ‘<brace-enclosed initializer list>’ to ‘std::atomic<void*>’
mem_block_cache block_cache = { 0, 0, BOOST_STATIC_MUTEX_INIT, };
^
make: *** [boost_regex/regex.o] Error 1
ERROR: compilation failed for package ‘flowCore’
* removing ‘/home/nitin/R/x86_64-pc-linux-gnu-library/3.3/flowCore’
ERROR: dependency ‘flowCore’ is not available for package ‘flowAI’
* removing ‘/home/nitin/R/x86_64-pc-linux-gnu-library/3.3/flowAI’
The downloaded source packages are in
‘/tmp/RtmpTbmU8h/downloaded_packages’
installation path not writeable, unable to update packages: mgcv, survival
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘flowCore’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘flowAI’ had non-zero exit status
Similarly afflicted (except on MacOSX) I find that I can successfully install from github, as:
library(devtools)
install_github("RGLab/flowCore",ref='trunk')
FWIW, the issue is more aptly resolved in MacOS by installing R using the CRAN build of R, instead of from homebrew, as I had previously.