> # 设置清华CRAN镜像
> options(repos = c(CRAN = "http://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
> # 安装基础依赖（引用[2]方法）
> install.packages(c("BiocManager", "GenomeInfoDbData"))
Error in install.packages : Updating loaded packages
> install.packages(c("BiocManager", "GenomeInfoDbData"))
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Warning in install.packages :
package ‘GenomeInfoDbData’ is not available for this version of R
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
There is a binary version available but the source version
is later:
binary source needs_compilation
BiocManager 1.30.20 1.30.26 FALSE
installing the source package ‘BiocManager’
trying URL 'http://mirrors.tuna.tsinghua.edu.cn/CRAN/src/contrib/BiocManager_1.30.26.tar.gz'
Content type 'application/octet-stream' length 594489 bytes (580 KB)
downloaded 580 KB
* installing *source* package 'BiocManager' ...
** package 'BiocManager' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BiocManager'
finding HTML links ... done
BiocManager-package html
available html
install html
repositories html
valid html
version html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)
Making 'packages.html' ... done
The downloaded source packages are in
‘C:\Users\Administrator\AppData\Local\Temp\RtmpyqErlw\downloaded_packages’
> # 通过BiocManager安装生物信息学依赖（引用[4]方法）
> if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
Bioconductor version 3.14 (BiocManager 1.30.26), R 4.1.2
(2021-11-01)
Bioconductor version '3.14' is out-of-date; the current release
version '3.21' is available with R version '4.5'; see
https://bioconductor.org/install
> # 设置中科大Bioconductor镜像（关键步骤）
> options(BioC_mirror = "http://mirrors.ustc.edu.cn/bioc/")
> # 安装核心依赖包
> BiocManager::install(c("genefilter", "sva", "Biobase"))
'getOption("repos")' replaces Bioconductor standard repositories,
see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: http://mirrors.tuna.tsinghua.edu.cn/CRAN/
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/bioc/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/annotation/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/experiment/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/workflows/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/workflows/src/contrib/PACKAGES'
Bioconductor version 3.14 (BiocManager 1.30.26), R 4.1.2
(2021-11-01)
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/bioc/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/annotation/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/experiment/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository http://mirrors.ustc.edu.cn/bioc//packages/3.14/workflows/src/contrib:
cannot open URL 'http://mirrors.ustc.edu.cn/bioc//packages/3.14/workflows/src/contrib/PACKAGES'
Old packages: 'backports', 'boot', 'class', 'cli', 'cluster',
'codetools', 'dplyr', 'farver', 'foreign', 'ggrepel', 'glue',
'KernSmooth', 'lattice', 'lme4', 'mgcv', 'minqa', 'nlme',
'nloptr', 'nnet', 'purrr', 'quantreg', 'rbibutils', 'Rcpp',
'RcppEigen', 'rlang', 'rpart', 'SparseM', 'spatial', 'stringi',
'survival', 'tibble', 'tidyr', 'tidyselect', 'utf8', 'vctrs'
Update all/some/none? [a/s/n]:
n
Warning message:
package(s) not installed when version(s) same as or greater than
current; use `force = TRUE` to re-install: 'genefilter' 'sva'
'Biobase'
> force = TRUE
> # 按顺序加载测试
> library(GenomeInfoDbData) # 先前缺失的依赖（引用[1]）
Error in library(GenomeInfoDbData) :
there is no package called ‘GenomeInfoDbData’
> library(genefilter) # 原问题包
Error: package or namespace load failed for ‘genefilter’ in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'F:/R/R-4.1.2/R-4.1.2/library/Biobase/libs/x64/Biobase.dll':
LoadLibrary failure: 鎵句笉鍒版寚瀹氱殑绋嬪簭銆
In addition: Warning message:
package ‘genefilter’ was built under R version 4.5.0
> library(sva) # 目标包
Loading required package: genefilter
Error: package or namespace load failed for ‘genefilter’ in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'F:/R/R-4.1.2/R-4.1.2/library/Biobase/libs/x64/Biobase.dll':
LoadLibrary failure: 鎵句笉鍒版寚瀹氱殑绋嬪簭銆
Error: package ‘genefilter’ could not be loaded
In addition: Warning messages:
1: package ‘sva’ was built under R version 4.5.0
2: package ‘genefilter’ was built under R version 4.5.0
> library(Biobase) # sva的依赖（引用[4]）
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect,
is.element, setdiff, setequal, union
Attaching package: ‘BiocGenerics’
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, is.unsorted,
lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Error: package or namespace load failed for ‘Biobase’ in inDL(x, as.logical(local), as.logical(now), ...):
unable to load shared object 'F:/R/R-4.1.2/R-4.1.2/library/Biobase/libs/x64/Biobase.dll':
LoadLibrary failure: 鎵句笉鍒版寚瀹氱殑绋嬪簭銆
In addition: Warning messages:
1: package ‘Biobase’ was built under R version 4.5.0
2: package ‘BiocGenerics’ was built under R version 4.5.0
> 我需要下载适配R-4.1.2的sva包和genefilter包
本文探讨了解决使用Cabal安装Base包时遇到的版本过低及派生的错误问题，通过删除多余的Base版本来解决Distribution/Client/Dependency/TopDown.hs文件中的模式匹配不全错误。
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