无法正确安装/加载 Rcpp

编程问答 2022-06-02

问题描述

拼命地尝试加载和使用 Rcpp（其实我正在尝试使用需要 Rcpp 的包 Seurat）

> library(Seurat)
Error: package or namespace load Failed for ‘Seurat’ in loadNamespace(j <- i[[1L]],c(lib.loc,.libPaths()),versionCheck = vI[[j]]):
 there is no package called ‘Rcpp’
In addition: Warning message:
package ‘Seurat’ was built under R version 4.0.2 
> install.packages("Rcpp")
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/Rcpp_1.0.5.tgz'
Content type 'application/x-gzip' length 3215939 bytes (3.1 MB)
==================================================
downloaded 3.1 MB


The downloaded binary packages are in
    /var/folders/hl/247qzpv55z99f6kgddn95kk80000gn/T//RtmpX3Ovqt/downloaded_packages
> library(Rcpp)
Error: package or namespace load Failed for ‘Rcpp’ in dyn.load(file,DLLpath = DLLpath,...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so,6): Symbol not found: _EXTPTR_PTR
  Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
  Expected in: /Library/Frameworks/R.framework/Resources/lib/libR.dylib
 in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/libs/Rcpp.so
In addition: Warning message:
package ‘Rcpp’ was built under R version 4.0.2

我已经尝试了以下

  1. 重新启动、重新安装 -> 相同的错误
  2. 确保已安装 Xcode（从应用商店下载）
  3. 使用 xcode-select --install 从终端安装命令行工具
  4. 从源代码安装
> install.packages("Rcpp",type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_1.0.5.tar.gz'
Content type 'application/x-gzip' length 2950521 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c api.cpp -o api.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c attributes.cpp -o attributes.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c barrier.cpp -o barrier.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c date.cpp -o date.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c module.cpp -o module.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c rcpp_init.cpp -o rcpp_init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rcpp/00new/Rcpp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rcpp)

The downloaded source packages are in
    ‘/private/var/folders/hl/247qzpv55z99f6kgddn95kk80000gn/T/RtmpX3Ovqt/downloaded_packages’
> library(Rcpp)
Error: package or namespace load Failed for ‘Rcpp’ in get(Info[i,1],envir = env):
 lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/R/Rcpp.rdb' is corrupt
In addition: Warning message:
In get(Info[i,envir = env) : internal error -3 in R_decompress1

有人可以请教吗？ 谢谢！

解决方法

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rrrcppseurat