Mac M2环境下R 4.2.2加载affy包失败问题求助

报错信息 #

> library(affy)
Error: package or namespace load failed for ‘affy’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/libs/preprocessCore.so':
  dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/libs/preprocessCore.so, 0x0006): Library not loaded: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib'
  Referenced from: '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/preprocessCore/libs/preprocessCore.so'
  Reason: tried: '/opt/R/arm64/gfortran/lib/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file)

正常加载的包日志 #

> library(BiocManager)
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31)
> library('limma')
> library('GEOquery')
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:limma’:

    plotMA

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated,
    eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

环境与已执行操作 #

• 环境：Mac M2芯片，R版本4.2.2
• 已执行操作：
  • 删除/Library/Frameworks/R.framework/Resources/library路径下的affy文件夹后重装，仍报错；BiocManager、limma、GEOquery可正常加载。
  • 检查并更新所有包至最新版本。
  • 成功安装haven包。

原因分析 #

加载失败的核心问题是系统缺少适配arm64架构的gfortran运行库libgfortran.5.dylib。affy包依赖preprocessCore包，而preprocessCore编译时需要链接该库，但你的M2芯片系统在指定路径中找不到这个库，导致无法加载对应的共享对象文件。

解决步骤 #

1. 安装适配arm64的gfortran库
   打开终端，通过Homebrew安装gcc套件（包含所需gfortran库）：

   brew install gcc
   

2. 重建preprocessCore包
   先卸载现有包，再重新安装以确保链接到新库：

   remove.packages("preprocessCore")
   BiocManager::install("preprocessCore")
   

3. 重新加载affy包

   library(affy)
   

若上述步骤无效，可尝试：

• 用sessionInfo()确认R是arm64版本，避免混用x86_64架构的包。
• 强制清理缓存并重装affy及依赖：

  BiocManager::install("affy", force = TRUE, clean = TRUE)
  

内容的提问来源于stack exchange，提问作者nikkikki