安装 flowCore 包 R 时出错答案

【问题标题】：Error in installing flowCore package R安装 flowCore 包 R 时出错
【发布时间】：2016-11-26 14:43:36
【问题描述】：

我正在尝试在 R 3.3.2（Ubuntu 14.04 LTS）中安装 flowCore 包（Bioconductor 3.4）。但我收到以下错误。任何人都可以提出一些解决方案谢谢。

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

【问题讨论】：

我无法在使用 BiocInstaller::biocLite("flowCore") 的类似系统上重现此问题。错误似乎与boost有关？你安装了boost吗？ stackoverflow.com/questions/12578499/… 或者 BH 包 cran.r-project.org/web/packages/BH/index.html
在 Ubuntu 16.04 上对我来说同样的错误，使用 biocLite("flowCore") 安装 R 3.3.1 和 Bioconductor 3.3。
对我来说，当缺少开发库时，通常会出现类似的问题。尝试先安装开发加速launchpad.net/ubuntu/trusty/+package/libboost-regex-dev

标签： r bioconductor

【解决方案1】：

同样困扰（MacOSX除外）我发现我可以从github成功安装，为：

library(devtools)
install_github("RGLab/flowCore",ref='trunk')

FWIW，通过使用 R 的 CRAN 版本安装 R，而不是像以前那样从自制软件安装 R，这个问题在 MacOS 中得到了更恰当的解决。

【讨论】：