嘗試安裝 R 包時出錯：通用文件格式錯誤：切片內容不是 mach-o 或 static 庫文件

Question

當嘗試安裝涉及基因序列分析的 R 包（在 RStudio 和命令行 R 中）時，即猿，adegenet，蜘蛛，我收到以下錯誤：

ld: malformed universal file: slice content is not mach-o or a static library file '/usr/local/lib/libgfortran.dylib'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [ape.so] Error 1
ERROR: compilation failed for package ‘ape’

我嘗試了很多方法：重新安裝 Xcode，通過 Homebrew 重新安裝 gcc，但都沒有解決問題。 我在安裝 ape 時收到上述錯誤，但在安裝 adegenet 或 spider 時間歇性地收到鏈接警告，並且總是在安裝 adegenet 或 spider 時收到它們（例如ld: warning: object file (decorana.o) was built for newer macOS version (12.5) than being linked (12.0) ）。 我懷疑我的機器上存在的 gcc 版本沖突可能存在問題。 例如，終端中的命令which gcc返回/usr/bin/gcc盡管 brew-installed gcc 組件位於/usr/local/Cellar/gcc/ 。 我很困惑為什么會出現這種情況，因為/usr/local/在我的路徑中列在/usr/bin/之前。 當然，這可能不是唯一的問題。

我正在使用 MacOS 12.5、RStudio 2022.07.0、R 4.2.1，並且 brew 完全是最新的（例如 brew outdated 什么都不返回）。

任何和所有的幫助將不勝感激！

---

嘗試在 RStudio 中安裝猿的完整 output 如下：

> install.packages("ape")
Installing package into ‘/usr/local/lib/R/4.2/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/ape_5.6-2.tar.gz'
Content type 'application/x-gzip' length 1754486 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c BIONJ.c -o BIONJ.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c NNI.c -o NNI.o
clang++ -std=gnu++14 -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c SPR.c -o SPR.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c additive.c -o additive.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c ape.c -o ape.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c bNNI.c -o bNNI.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c bionjs.c -o bionjs.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c bipartition.c -o bipartition.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c bitsplits.c -o bitsplits.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c delta_plot.c -o delta_plot.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c dist_dna.c -o dist_dna.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c dist_nodes.c -o dist_nodes.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c ewLasso.c -o ewLasso.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c heap.c -o heap.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c mat_expo.c -o mat_expo.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c me.c -o me.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c me_balanced.c -o me_balanced.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c me_ols.c -o me_ols.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c mvr.c -o mvr.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c mvrs.c -o mvrs.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c nj.c -o nj.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c njs.c -o njs.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c pic.c -o pic.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c plot_phylo.c -o plot_phylo.o
clang++ -std=gnu++14 -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -g -O2  -c prop_part.cpp -o prop_part.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c rTrait.c -o rTrait.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c read_dna.c -o read_dna.o
clang++ -std=gnu++14 -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -g -O2  -c reorder_Rcpp.cpp -o reorder_Rcpp.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c reorder_phylo.c -o reorder_phylo.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c treePop.c -o treePop.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c tree_build.c -o tree_build.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c tree_phylo.c -o tree_phylo.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c triangMtd.c -o triangMtd.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c triangMtds.c -o triangMtds.o
clang -I"/usr/local/Cellar/r/4.2.1/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.2/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -Wno-implicit-function-declaration  -c ultrametric.c -o ultrametric.o
clang++ -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/Cellar/r/4.2.1/lib/R/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/xz/lib -L/usr/local/lib -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -L/usr/local/Cellar/r/4.2.1/lib/R/lib -lRlapack -L/usr/local/opt/openblas/lib -lopenblas -L/usr/local/opt/gcc/lib/gcc/11/gcc/x86_64-apple-darwin21/11 -L/usr/local/opt/gcc/lib/gcc/11/gcc -L/usr/local/opt/gcc/lib/gcc/11 -lgfortran -lemutls_w -lquadmath -lm -L/usr/local/Cellar/r/4.2.1/lib/R/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
ld: malformed universal file: slice content is not mach-o or a static library file '/usr/local/lib/libgfortran.dylib'
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [ape.so] Error 1
ERROR: compilation failed for package ‘ape’
* removing ‘/usr/local/lib/R/4.2/site-library/ape’
Warning in install.packages :
  installation of package ‘ape’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/4n/0ghjrzsd4g393zjlgxy9ympc0000gn/T/Rtmpot4Zet/downloaded_packages’

Answer 1

好吧...我刪除了/usr/local/lib/libgfortran.dylib因為它只是一個鏈接，這導致安裝程序在不同的目錄中找到libgfortran.dylib並且安裝僅使用鏈接文件警告。 我稱這是一場勝利。