R(MacOS10.8.5)，RcppArmadillo :无法找到鲤鱼库或符号_wrapper_ddot_

Question

安装"RcppArmadillo“使我非常失败，现在在"R”上安装了几个小时

R-2.3.1

和MACOS系统10.8.5：

Darwin 12.6.0 Darwin Kernel Version 12.6.0; xnu/RELEASE_X86_64 x86_64

现已编译并成功安装了Armadillo (6.100.0)。

这就是罪犯：

R> install.packages("RcppArmadillo", verbose=T)

编译OK，但未能成功加载包(作为构建时测试)。产出如下：

* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
* checking LAPACK_LIBS: divide-and-conquer complex SVD available via R-supplied LAPACK
** libs
g++ -I/opt/local/R.framework/Resources/include -DNDEBUG  -arch x86_64 -framework System -Wunused-command-line-argument-hard-error-in-future -I/opt/local/include -I/Users/.../usr/include -I/Users/.../usr/local/include -I/opt/X11/include -Wunused-command-line-argument-hard-error-in-future -I"/opt/local/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -I../inst/include -fPIC  -arch x86_64 -framework System -Wunused-command-line-argument-hard-error-in-future -I/opt/local/include -I/Users/.../usr/include -I/Users/.../usr/local/include -I/opt/X11/include -Wunused-command-line-argument-hard-error-in-future  -c RcppArmadillo.cpp -o RcppArmadillo.o
clang: warning: -framework System: 'linker' input unused
clang: warning: -framework System: 'linker' input unused
g++ -I/opt/local/R.framework/Resources/include -DNDEBUG  -arch x86_64 -framework System -Wunused-command-line-argument-hard-error-in-future -I/opt/local/include -I/Users/.../usr/include -I/Users/.../usr/local/include -I/opt/X11/include -Wunused-command-line-argument-hard-error-in-future -I"/opt/local/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -I../inst/include -fPIC  -arch x86_64 -framework System -Wunused-command-line-argument-hard-error-in-future -I/opt/local/include -I/Users/.../usr/include -I/Users/.../usr/local/include -I/opt/X11/include -Wunused-command-line-argument-hard-error-in-future  -c RcppExports.cpp -o RcppExports.o
clang: warning: -framework System: 'linker' input unused
clang: warning: -framework System: 'linker' input unused
g++ -I/opt/local/R.framework/Resources/include -DNDEBUG  -arch x86_64 -framework System -Wunused-command-line-argument-hard-error-in-future -I/opt/local/include -I/Users/.../usr/include -I/Users/.../usr/local/include -I/opt/X11/include -Wunused-command-line-argument-hard-error-in-future -I"/opt/local/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -I../inst/include -fPIC  -arch x86_64 -framework System -Wunused-command-line-argument-hard-error-in-future -I/opt/local/include -I/Users/.../usr/include -I/Users/.../usr/local/include -I/opt/X11/include -Wunused-command-line-argument-hard-error-in-future  -c fastLm.cpp -o fastLm.o
clang: warning: -framework System: 'linker' input unused
clang: warning: -framework System: 'linker' input unused
g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/R.framework/Resources/lib -arch x86_64 -framework System -Wunused-command-line-argument-hard-error-in-future -L/opt/local/lib -L/Users/.../usr/lib -L/Users/.../usr/lib -L/opt/X11/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/opt/local/R.framework/Resources/lib -lRlapack -L/opt/local/R.framework/Resources/lib -lRblas -F/opt/local/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation
installing to /opt/local/R.framework/Versions/3.2/Resources/library/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/opt/local/R.framework/Versions/3.2/Resources/library/RcppArmadillo/libs/RcppArmadillo.so':
  dlopen(/opt/local/R.framework/Versions/3.2/Resources/library/RcppArmadillo/libs/RcppArmadillo.so, 6): Symbol not found: _wrapper_ddot_
  Referenced from: /opt/local/R.framework/Versions/3.2/Resources/library/RcppArmadillo/libs/RcppArmadillo.so
  Expected in: flat namespace
 in /opt/local/R.framework/Versions/3.2/Resources/library/RcppArmadillo/libs/RcppArmadillo.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/local/R.framework/Versions/3.2/Resources/library/RcppArmadillo’

因此，简而言之，它需要符号"_wrapper_ddot_“，这是它找不到的。但是这个符号在/opt/local/lib/libarmadyar.6.dylib中，该符号已成功安装。例如：

命令：

nm /opt/local/lib/libarmadillo.6.dylib | grep _wrapper_ddot_

产出：

/opt/local/lib/libarmadillo.6.dylib
00000000000023e0 T _wrapper_ddot_

然后创建一个~/.R/Makevars，其中包含：

PKG_LIBS += -L/opt/local/lib -larmadillo

尝试使用以下方法再次安装：

R> install.packages("RcppArmadillo")

再次编译OK，但现在它无法加载armadillo dylib，并给出以下错误消息：

...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/private/tmp/RtmpqEsodh/Rinst62b64deb7e7/RcppArmadillo/libs/RcppArmadillo.so':
  dlopen(/private/tmp/RtmpqEsodh/Rinst62b64deb7e7/RcppArmadillo/libs/RcppArmadillo.so, 6): Library not loaded: libarmadillo.6.dylib
  Referenced from: /private/tmp/RtmpqEsodh/Rinst62b64deb7e7/RcppArmadillo/libs/RcppArmadillo.so
  Reason: image not found
Error: loading failed

我甚至手动编译了包，跳过测试，然后安装。不是的！它总是抱怨说它无法加载鲤鱼库或找不到符号"_wrapper_ddot_“。

然而，(依赖)鲤鱼库是存在的：

ls -al /opt/local/lib/libarmadillo.6.10.0.dylib

-rwxr-xr-x  1 root  admin  5... /opt/local/lib/libarmadillo.6.10.0.dylib

(以及与它的各种符号链接，例如6.dylib和just dylib)

将~/.R/Makevars设置为：

PKG_LIBS += -larmadillo
CFLAGS += ${PKG_LIBS}
CXXFLAGS += ${PKG_LIBS}

从这方面没有带来好消息(我现在很绝望)。

最后，我编写了一个小的c程序，用于dlopen() armadillo库(dylib)。取决于我使用它的模式是成功还是失败，如下所示：

trying : mode 2 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 2 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 1 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 1 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 8 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 8 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 4 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 4 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 18 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    error for mode 18 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'    err: Undefined error: 0
trying : mode 17 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    error for mode 17 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'    err: Undefined error: 0
trying : mode 24 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    error for mode 24 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'    err: Undefined error: 0
trying : mode 20 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    error for mode 20 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'    err: Undefined error: 0
trying : mode 130 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 130 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 129 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 129 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 136 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 136 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 132 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 132 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 258 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 258 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 257 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 257 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 264 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 264 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
trying : mode 260 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'
    success: mode 260 and lib '/opt/local/lib/libarmadillo.6.10.0.dylib'

使用各种模式测试加载armadillo库的C程序是：

#include <stdio.h>
#include <string.h>
#include <errno.h>
#include <dlfcn.h>

int main(void){
    char lib[] = "/opt/local/lib/libarmadillo.6.10.0.dylib";
    int modes[] = {
        RTLD_NOW, RTLD_LAZY, RTLD_GLOBAL, RTLD_LOCAL,
        RTLD_NOW|RTLD_NOLOAD, RTLD_LAZY|RTLD_NOLOAD, RTLD_GLOBAL|RTLD_NOLOAD, RTLD_LOCAL|RTLD_NOLOAD,
        RTLD_NOW|RTLD_NODELETE, RTLD_LAZY|RTLD_NODELETE, RTLD_GLOBAL|RTLD_NODELETE, RTLD_LOCAL|RTLD_NODELETE,
        RTLD_NOW|RTLD_FIRST, RTLD_LAZY|RTLD_FIRST, RTLD_GLOBAL|RTLD_FIRST, RTLD_LOCAL|RTLD_FIRST
    };


    for(int modeI=0;modeI<16;modeI++){
        int mode = modes[modeI];
        void    *ahandle;
        printf("trying : mode %d and lib '%s'\n", mode, lib);
        if( (ahandle=dlopen(lib, mode)) == NULL ){
            fprintf(stderr, "\terror for mode %d and lib '%s'", mode, lib);
            printf("\terr: %s\n", strerror(errno));
        } else {
            dlclose(ahandle);
            printf("\tsuccess: mode %d and lib '%s'\n", mode, lib);
        }
    }
}

问题是:为什么R不加载armadillo库？是否有一个与LD_LIBRARY_PATH等价的R？

其他软件包安装正常(大约30个软件包)。

此外，armadillo C++程序编译并运行OK：

#include <iostream>
#include <armadillo>

using namespace std;
using namespace arma;

int main(int argc, char** argv)
  {
  mat A = randu<mat>(4,5);
  mat B = randu<mat>(4,5);

  cout << A*trans(B) << endl;

  return 0;
  }

使用

g++ -I/opt/local/include -L/opt/local/lib arma.c -larmadillo

非常感谢，

Answer 1

经过两年半的时间，该问题再次出现，解决方案仍然有效和相关。在OSX中，R-3.4.3拒绝安装血腥的RcppArmadillo，除非我首先通过port uninstall armadillo移除鲤鱼系统包(而不是R包)。

所以,

port uninstall armadillo

兄弟们