包安裝錯誤：編譯失敗

Question

我最近將 R 更新為 3.1.0。 我試圖將我的包移動到 R.Framework 中的 3.1（我正在運行 OSX Mavericks）並且不知何故弄得一團糟，所以在全新安裝之前完全卸載了所有內容。

重新安裝軟件包時，我沒有任何問題，直到我遇到了產生以下錯誤的forecast軟件包：

     package ‘forecast’ is available as a source package but not as a binary

Warning in install.packages :
package ‘forecast’ is not available (for R version 3.1.0)

我實際上有 R 3.1.0 並且在重新安裝之前預測和 hts 一起工作，所以我懷疑問題源於我所做的事情，而不是兼容性問題。

我運行了以下命令以查看是否可以發現有關安裝失敗的更多詳細信息： install.packages("forecast", type = "source", verbose = T, quiet = F)

其輸出有點超出我的范圍，但可能有助於診斷：

system (cmd0): /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL
trying URL 'http://cran.rstudio.com/src/contrib/forecast_5.3.tar.gz'
Content type 'application/x-gzip' length 150395 bytes (146 Kb)
opened URL
==================================================
downloaded 146 Kb

foundpkgs: forecast, /var/folders/0y/_13fkvws0tn5xh4m8wsymkdh0000gp/T//RtmpzTzSpG/downloaded_packages/forecast_5.3.tar.gz
files: /var/folders/0y/_13fkvws0tn5xh4m8wsymkdh0000gp/T//RtmpzTzSpG/downloaded_packages/forecast_5.3.tar.gz
* installing *source* package ‘forecast’ ...
** package ‘forecast’ successfully unpacked and MD5 sums checked
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c calcBATS.cpp -o calcBATS.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c calcTBATS.cpp -o calcTBATS.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c etsTargetFunction.cpp -o etsTargetFunction.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c etsTargetFunctionWrapper.cpp -o etsTargetFunctionWrapper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c etscalc.c -o etscalc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c etspolyroot.c -o etspolyroot.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c makeBATSMatrices.cpp -o makeBATSMatrices.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c makeTBATSMatrices.cpp -o makeTBATSMatrices.o
makeTBATSMatrices.cpp:11:6: warning: unused variable 'lengthSeasonal' [-Wunused-variable]
        int lengthSeasonal = 0;
            ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c updateMatrices.cpp -o updateMatrices.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c updateTBATSMatrices.cpp -o updateTBATSMatrices.o
updateTBATSMatrices.cpp:38:10: warning: unused variable 'gammaVector' [-Wunused-variable]
        double *gammaVector;
                ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o forecast.so calcBATS.o calcTBATS.o etsTargetFunction.o etsTargetFunctionWrapper.o etscalc.o etspolyroot.o makeBATSMatrices.o makeTBATSMatrices.o updateMatrices.o updateTBATSMatrices.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [forecast.so] Error 1
ERROR: compilation failed for package ‘forecast’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/forecast’
Warning in install.packages :
  installation of package ‘forecast’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/0y/_13fkvws0tn5xh4m8wsymkdh0000gp/T/RtmpzTzSpG/downloaded_packages’

我真的很感激這里的一些幫助。 我最近處理的大部分代碼都依賴於預測中的函數。

Answer 1

這是我所做的（ OS X Mavericks 上的 RcppArmadillo 編譯錯誤）

1. 從 brew 安裝 gfortran（如果你沒有 brew，谷歌它。安裝很簡單）：

   brew install gfortran

   如果已安裝，請使用以下命令升級到最新版本：

   brew upgrade gfortran

2. 然后執行以下操作之一：

   ln -s /usr/local/Cellar/gfortran/4.8.2/gfortran/lib/libgfortran.* /usr/local/lib/

   或將此行添加到~/.R/Makevars文件中：

   FLIBS=-L/usr/local/Cellar/gfortran/4.8.2/gfortran

   我做了第二個選擇。

3. 現在再次運行install.packages("forecast", type = "source")它應該可以工作。

Answer 2

就我而言，我試圖用devtools::install_github("robjhyndman/forecast")安裝最新版本的 {forecast} 包，但遇到了類似的錯誤。

然后，雖然我不確定我所做的是否正確，但按照 mchangun 的回答，我做了如下操作並解決了錯誤：

1. brew upgrade gcc

錯誤：gcc 5.2.0 已經安裝

2. gcc --version

配置為：--prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/ MacOSX10.11.sdk/usr/include/c++/4.2.1 Apple LLVM version 7.0.0 (clang-700.1.76) 目標：x86_64-apple-darwin15.0.0 線程模型：posix

3. ls /usr/local/Cellar/gcc

4.9.2 4.9.2_1 5.2.0

4. 將FLIBS=-L/usr/local/Cellar/gcc/5.2.0到~/.R/Makevars文件

5. 運行devtools::install_github("robjhyndman/forecast")並且它起作用了。

Answer 3

終端

1. 釀造安裝gcc
2. gcc --version
3. ls /usr/local/Cellar/gcc 6.3.0_1
4. 須藤 vi /Library/Frameworks/R.framework/Resources/etc/Makeconf
5. 添加行 FLIBS=-L/usr/local/Cellar/gcc/6.3.0_1

工作室：

6. install.packages("預測"

Answer 4

從https://gcc.gnu.org/wiki/GFortranBinariesMacOS下載 gfortran

須藤 rm -r /usr/local/gfortran /usr/local/bin/gfortran

然后安裝gfortran

須藤 vi /Library/Frameworks/R.framework/Resources/etc/Makeconf

將所有 gfortran-4.8 更改為 gfortran

FC = gfortran FCFLAGS = -Wall -g -O2 $(LTO) FCLIBS = F77 = gfortran F77_VISIBILITY = FFLAGS = -g -O2 $(LTO)

FLIBS = -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm

將上面的 FLIBS 更改為下面的

FLIBS = -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm

Answer 5

要安裝 gfortran，請使用

brew cask install gfortran