R包安装在所有机器上成功，但一台答案

【问题标题】：R package installation is successful on all machines but oneR包安装在所有机器上成功，但一台
【发布时间】：2012-06-28 17:32:00
【问题描述】：

我们是一个致力于包含 C/C++ 代码的 R 包的团队。该软件包可以成功安装在除一台机器之外的所有机器上。这些都运行相同版本的 Mac OS X。我提供了在我的计算机（成功）和同事的计算机（错误）上安装软件包的日志文件。该包依赖于Rcpp包和GSL库，两台机器都安装成功。

我的电脑

WARNING: ignoring environment value of R_HOME
* installing to library '/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15'
* installing *source* package 'mrenci' ...
** libs
*** arch - x86_64
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include"   -fPIC  -pipe -O2 -m64  -c MRMRTree.cc -o MRMRTree.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include"   -fPIC  -pipe -O2 -m64  -c Matrix.cc -o Matrix.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include"   -fPIC  -pipe -O2 -m64  -c MiMBuilder.cc -o MiMBuilder.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include"   -fPIC  -pipe -O2 -m64  -c SymmetricMatrix.cc -o SymmetricMatrix.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include"   -fPIC  -pipe -O2 -m64  -c adaptor.cc -o adaptor.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include"   -fPIC  -pipe -O2 -m64  -c memory.cc -o memory.o
/opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -fopenmp -fopenmp -I/opt/local/include -I"/Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/include"   -fPIC  -pipe -O2 -m64  -c tools.cc -o tools.o
/opt/local/bin/g++-mp-4.5 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/lib -o mrenci.so MRMRTree.o Matrix.o MiMBuilder.o SymmetricMatrix.o adaptor.o memory.o tools.o /Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/Rcpp/lib/x86_64/libRcpp.a -fopenmp -fopenmp -L/opt/local/lib/R/lib/x86_64 -lR
installing to /Users/dejayn/R/x86_64-apple-darwin10.8.0-library/2.15/mrenci/libs/x86_64
** R
** preparing package for lazy loading
** testing if installed package can be loaded

* DONE (mrenci)

同事的电脑

WARNING: ignoring environment value of R_HOME
* installing to library '/Library/Frameworks/R.framework/Versions/2.15/Resources/library'
* installing *source* package 'mrenci' ...
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c MRMRTree.cc -o MRMRTree.o
MRMRTree.cc: In member function 'double* const MRMRTree::bootstrap(unsigned int)':
MRMRTree.cc:73: warning: iteration variable 'i' is unsigned
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c Matrix.cc -o Matrix.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c MiMBuilder.cc -o MiMBuilder.o
MiMBuilder.cc: In member function 'Matrix* const MiMBuilder::createMiM(unsigned int*, unsigned int, unsigned int*, unsigned int)':
MiMBuilder.cc:102: warning: iteration variable 'i' is unsigned
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c SymmetricMatrix.cc -o SymmetricMatrix.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c adaptor.cc -o adaptor.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c memory.cc -o memory.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -fopenmp -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include"   -fPIC  -g -O2  -c tools.cc -o tools.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o mrenci.so MRMRTree.o Matrix.o MiMBuilder.o SymmetricMatrix.o adaptor.o memory.o tools.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/lib/x86_64/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64
** R
** preparing package for lazy loading
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so':
  dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so, 6): Symbol not found: _GOMP_critical_name_end
  Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so
  Expected in: flat namespace
 in /Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci/libs/x86_64/mrenci.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/mrenci'

起初，在我同事的计算机上安装会导致编译两种架构的包，g++ 抱怨未知的-arch 参数。然而，这个问题似乎已经通过强制定位单一架构x86_64 得到缓解。还值得注意的是，由于这些错误，所有计算机现在都有多个版本的 R 和 g++。这是链接器的问题吗？ R 及其包是否需要使用相同的编译器？就我的电脑而言，我从未明确要求使用 g++-mp-4.5 而不是默认的 g++（4.2 版），所以我认为 R 会自动检测到它。

如果这有任何帮助，以下是我的 Makevars 包含的内容：

PKG_LIBS=`$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(SHLIB_OPENMP_CFLAGS) -fopenmp
PKG_CPPFLAGS=$(SHLIB_OPENMP_CXXFLAGS) -fopenmp
PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS) -fopenmp

$(SHLIB_OPENMP_*FLAGS) 标志似乎只在我的计算机上定义；明确添加了-fopenmp 标志，以便该包可以在所有机器上运行。

有没有人遇到过类似的问题？任何帮助将不胜感激。

【问题讨论】：

这个问题似乎还缺少很多细节。
告诉我缺少哪些细节，我会尽力提供。
XCode 的版本？ .Rprofile 文件似乎也不同，因为被引用的库似乎不同。
这是我第一次在 Mac OS X 上工作，所以我有点迷茫。如何找到.Rprofile？我们都在使用 Xcode 3.2，但现在通过 MacPorts 安装了更新版本的 gcc（4.5、4.6、4.7）。
（MacPorts 安装的所需文件可能位于 R 不期望的目录中。）名称以“.”开头的文件默认隐藏。我运行 Finder 以显示这些文件。要执行该类型：defaults write com.apple.Finder AppleShowAllFiles YES 然后您需要重新启动 Finder.app 以获取要读取的参数（但以后不需要）：-click-hold> 在 Dock-Finder-icon 上，选择重新启动跨度>

标签： macos r linker compiler-errors g++

【解决方案1】：

我更改了同事的~/.R/Makevars 以符合我的配置

LDFLAGS=-L/opt/local/lib
CC=/opt/local/bin/gcc-mp-4.5 -std=gnu99
CXX=/opt/local/bin/g++-mp-4.5
CPP=/opt/local/bin/gcc-mp-4.5 -std=gnu99 -E
CXXCPP=/opt/local/bin/g++-mp-4.5 -E
CFLAGS=-pipe -O2 -m64
CXXFLAGS=-pipe -O2 -m64
SHLIB_CXXLD=/opt/local/bin/g++-mp-4.5
SHLIB_CXXLDFLAGS=-dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress
SHLIB_LD=/opt/local/bin/gcc-mp-4.5 -std=gnu99
SHLIB_LDFLAGS=-dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress

此外，发出安装命令时使用了--no-multiarch 参数。它现在可以在他的电脑上运行。

问题是因为 openMP 的使用在代码内部是硬连线的（没有检查），而clang 在我问这个问题的同时不支持 openMP。当我们尝试通过 Mac 端口使用 gcc 时，我同事的 R 是使用默认 (Xcode) 编译器安装的。

【讨论】：