Error in installing flowCore package R

Question

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

I can't reproduce this on a similar system using `BiocInstaller::biocLite("flowCore")`. Error seems related to boost? Do you have boost installed? http://stackoverflow.com/questions/12578499/how-to-install-boost-on-ubuntu or perhaps BH package https://cran.r-project.org/web/packages/BH/index.html — user20650, Nov 23 '16 at 18:22
Same error for me on Ubuntu 16.04, with R 3.3.1 and Bioconductor 3.3 installing with `biocLite("flowCore")`. — bli, Nov 28 '16 at 13:27
For me this similar problems typically occur when a Development library is missing. Try installing the development boost first https://launchpad.net/ubuntu/trusty/+package/libboost-regex-dev — Jim Raynor, Nov 30 '16 at 13:19

malcook · Accepted Answer · 2016-11-25T21:55:45.733

2

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.

edited Nov 25 '16 at 21:55

answered Nov 25 '16 at 19:34

malcook

1,686
16
16

score 0 · Answer 2 · answered Jun 15 '23 at 13:01

This sequence worked on a fresh EC2 Ubuntu instance:

sudo R -e "install.packages('BiocManager')"
sudo R -e "BiocManager::install('flowCore', Ncpus = 8)" # will fail but still necessary
sudo R -e "install.packages('remotes')"
sudo R -e "remotes::install_github('RGLab/cytolib')"
sudo R -e "install.packages('cpp11')"
wget https://bioconductor.org/packages/release/bioc/src/contrib/flowCore_2.12.0.tar.gz
sudo R -e "install.packages('flowCore_2.12.0.tar.gz', repos = NULL, type = 'source', Ncpus = 8)"
sudo R -e "remove.packages(c('BiocManager', 'remotes'))"
rm flowCore_2.10.0.tar.gz

Error in installing flowCore package R

2 Answers2