编译 Rcpp 时遇到问题答案

【问题标题】：Trouble Compiling Rcpp编译 Rcpp 时遇到问题
【发布时间】：2015-10-23 03:51:00
【问题描述】：

我在 CentOS 6.5 机器上安装 Rcpp for R 3.2.2 时遇到了一些问题。我在 StackOverflow 和其他论坛上找到了并没有真正帮助的答案，这些论坛在解决这个问题方面似乎没有提供太多帮助。如果我尝试使用R CMD INSTALL从R内部或命令行安装，我最终会遇到类似的错误，即无法安装Rcpp，最终错误为make: *** [Date.o] Error 1，之前的行/错误为/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:35: error: expected declaration before end of line .

下面是我在从https://cran.rstudio.com/src/contrib/ 获取压缩包后尝试通过R CMD INSTALL Rcpp_0.12.1.tar.gz 安装。

$ sudo R CMD INSTALL Rcpp_0.12.1.tar.gz
* installing to library ‘/usr/lib64/R/library’
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Date.cpp -o Date.o
In file included from ../inst/include/Rcpp/platform/compiler.h:100,
                 from ../inst/include/Rcpp/r/headers.h:48,
                 from ../inst/include/RcppCommon.h:29,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:43:28: error: bits/c++config.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tree.h:63,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/map:60,
                 from ../inst/include/Rcpp/platform/compiler.h:176,
                 from ../inst/include/Rcpp/r/headers.h:48,
                 from ../inst/include/RcppCommon.h:29,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h:48:31: error: bits/c++allocator.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:42,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:40,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iterator:65,
                 from ../inst/include/RcppCommon.h:49,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h:42:76: error: bits/c++locale.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h:41,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:43,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:40,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iterator:65,
                 from ../inst/include/RcppCommon.h:49,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h:34:23: error: bits/gthr.h: No such file or directory
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h:35:30: error: bits/atomic_word.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h:39,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:45,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:40,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iterator:65,
                 from ../inst/include/RcppCommon.h:49,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h:43:30: error: bits/ctype_base.h: No such file or directory
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h:1510:31: error: bits/ctype_inline.h: No such file or directory
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:44,
                 from ../inst/include/Rcpp/platform/compiler.h:100,
                 from ../inst/include/Rcpp/r/headers.h:48,
                 from ../inst/include/RcppCommon.h:29,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:69: error: expected constructor, destructor, or type conversion before ‘(’ token
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:74: error: ‘_GLIBCXX_END_NAMESPACE’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:87: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:110: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:125: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:145: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:152: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:159: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:166: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:198: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:205: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:212: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:219: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:226: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:233: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:240: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:247: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:265: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:272: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:279: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:296: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:310: error: ‘__gnu_cxx’ was not declared in this scope
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:311: error: template argument 1 is invalid
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:355: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:378: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:385: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:392: error: ‘__true_type’ does not name a type
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h:417: error: ‘_GLIBCXX_END_NAMESPACE’ does not name a type
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:45,
                 from ../inst/include/Rcpp/platform/compiler.h:100,
                 from ../inst/include/Rcpp/r/headers.h:48,
                 from ../inst/include/RcppCommon.h:29,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:45: error: ‘__enable_if’ is not a template
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:64: error: ‘__is_integer’ is not a member of ‘std’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:64: error: ‘__is_integer’ is not a member of ‘std’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:64: error: template argument 1 is invalid
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:64: error: typedef name may not be a nested-name-specifier
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:64: error: expected ‘;’ before ‘>’ token
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:67: error: ‘__if_type’ has not been declared
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:107: error: ‘__is_integer’ is not a member of ‘std’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:107: error: ‘__is_integer’ is not a member of ‘std’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:107: error: template argument 1 is invalid
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:107: error: typedef name may not be a nested-name-specifier
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:107: error: expected ‘;’ before ‘>’ token
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:110: error: ‘__if_type’ has not been declared
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:158: error: ‘__is_integer’ is not a member of ‘std’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:158: error: expected primary-expression before ‘>’ token
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:158: error: expected constructor, destructor, or type conversion before ‘>’ token
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h:163: error: ‘__promote’ is not a template
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath:46,
                 from ../inst/include/Rcpp/platform/compiler.h:100,
                 from ../inst/include/Rcpp/r/headers.h:48,
                 from ../inst/include/RcppCommon.h:29,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/include/math.h:30: error: expected constructor, destructor, or type conversion before ‘extern’
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios:40,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:40,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iterator:65,
                 from ../inst/include/RcppCommon.h:49,
                 from ../inst/include/Rcpp.h:27,
                 from Date.cpp:31:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception:35: error: expected declaration before end of line
make: *** [Date.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/usr/lib64/R/library/Rcpp’

我尝试过的其他事情

已验证已安装 gcc.x86_64、gcc-c++.x86_64 和 gcc-gfortran.x86_64
已验证 make 和 automake 已安装

【问题讨论】：

你可能需要升级你的编译器；不幸的是，CentOS 6 附带了一个相当过时的 gcc 版本。 This 可能会有所帮助。
@nrussell 这绝对值得一试，但不幸的是，这并没有成功，即使启用了 SCL，仍然会看到同样的错误。
@nrussell 所以这对我来说是一个菜鸟之举。你是对的，使用 SCL 实际上确实解决了这个问题。当我最初使用 scl enable devtoolset-1.1 bash 切换到 SCL 时，我自己也是这样做的，但是当我 sudo 安装时并没有延续。

标签： c++ linux r gcc centos

【解决方案1】：

正如comments above 中指出的那样，诀窍是通过 SCL 使用新版本的编译器。

以下步骤改编自Ask Xmodulo上的此页面。

$ sudo wget http://people.centos.org/tru/devtools-1.1/devtools-1.1.repo -P /etc/yum.repos.d
$ sudo sh -c 'echo "enabled=1" >> /etc/yum.repos.d/devtools-1.1.repo'

在 RHEL6 上，您可能需要更新已安装的 .repo 文件以手动将 baseurl 设置为 http://people.centos.org/tru/devtools-1.1/6/$basearch/RPMS。从那里：

$ sudo yum install devtoolset-1.1

要安装系统范围的 R 库，您需要以 root 身份运行它，因此执行 scl enable devtoolset-1.1 bash 然后运行 sudo R 将运行应用程序，但未启用 SCL。所以改为：

$ sudo scl enable devtoolset-1.1 bash

这将以启用 SCL 的 root 身份启动 bash shell。最后，您可以使用以下命令安装库：

# R CMD INSTALL Rcpp_0.12.1.tar.gz

【讨论】：