在R 4.2.2环境下无法从Bioconductor 3.16下载flowUtils包求助

问题描述 #

在Windows 11笔记本的RStudio中，使用BiocManager 1.30.19从Bioconductor 3.16安装flowUtils包失败，已确认该包适配此Bioconductor版本，但仍无法完成下载。

问题代码 #

# 出现问题的代码
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("flowUtils", type = "binary")

代码运行输出 #

> if (!require("BiocManager", quietly = TRUE))
+     install.packages("BiocManager")
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
> 
> BiocManager::install("flowUtils")
Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'flowUtils'
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.2/library
  packages:
    boot, Matrix
Old packages: 'xfun'
Update all/some/none? [a/s/n]: a
trying URL 'https://cloud.r-project.org/bin/windows/contrib/4.2/xfun_0.35.zip'
Content type 'application/zip' length 406240 bytes (396 KB)
downloaded 396 KB

package ‘xfun’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘xfun’
Warning: restored ‘xfun’

The downloaded binary packages are in
        C:\Users\zaqai\AppData\Local\Temp\Rtmp6NbbuT\downloaded_packages
Warning messages:
1: package ‘flowUtils’ is not available for Bioconductor version '3.16'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
2: In file.copy(savedcopy, lib, recursive = TRUE) :
  problem copying C:\Users\zaqai\AppData\Local\R\win-library\4.2\00LOCK\xfun\libs\x64\xfun.dll to C:\Users\zaqai\AppData\Local\R\win-library\4.2\xfun\libs\x64\xfun.dll: Permission denied

会话信息 #

sessionInfo()

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_India.utf8  LC_CTYPE=English_India.utf8    LC_MONETARY=English_India.utf8 LC_NUMERIC=C                   LC_TIME=English_India.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.19

loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2

解决建议 #

• 解决权限冲突：右键RStudio图标选择「以管理员身份运行」，重新执行安装命令；或者指定用户目录作为安装路径：

  BiocManager::install("flowUtils", lib = "C:/Users/zaqai/AppData/Local/R/win-library/4.2")
  

  安装完成后用library(flowUtils, lib.loc = "C:/Users/zaqai/AppData/Local/R/win-library/4.2")加载包。

• 刷新Bioconductor索引：先验证当前Bioconductor环境，再跳过包更新直接安装flowUtils：

  BiocManager::valid()
  BiocManager::install("flowUtils", update = FALSE)
  

• 手动下载安装：找到对应Bioconductor 3.16版本的flowUtils二进制包，在RStudio中通过「Tools」→「Install Packages」选择本地包文件完成安装。

内容的提问来源于stack exchange，提问作者Zoya Qaiyum