BSgenome.Hsapiens.UCSC.hg38是生信技能树TCGA课程中讲到的需要使用的一个R包，所以我装了一个，发现这个包十分不好安装，现记录过程如下，方便后续使用。

1.第一次安装

> options("repos"="https://mirrors.ustc.edu.cn/CRAN/")
> if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
载入需要的程辑包：BiocManager
Bioconductor version 3.12 (BiocManager 1.30.10),
  ?BiocManager::install for help
> options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
> if(!require(BSgenome))BiocManager::install("BSgenome")

安装过程如下：

载入需要的程辑包：BSgenome
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3
  (2020-10-10)
Installing package(s) 'BSgenome'
试开URL’https://mirrors.ustc.edu.cn/bioc//packages/3.12/bioc/bin/windows/contrib/4.0/BSgenome_1.58.0.zip'
Content type 'application/zip' length 7624307 bytes (7.3 MB)
downloaded 7.3 MB

package ‘BSgenome’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\zzu\AppData\Local\Temp\RtmpgtI2Si\downloaded_packages
Installation path not writeable, unable to update packages:
  boot, class, codetools, foreign, KernSmooth, Matrix, nlme,
  nnet, spatial
Old packages: 'backports', 'BH', 'brio', 'broom', 'caTools',
  'cli', 'coin', 'cpp11', 'crayon', 'crosstalk', 'data.table',
  'DBI', 'dbplyr', 'DelayedArray', 'deldir', 'diffobj', 'dplyr',
  'DT', 'edgeR', 'enrichplot', 'fansi', 'fastmap', 'findpython',
  'flextable', 'forcats', 'future.apply', 'gert', 'ggrepel',
  'ggridges', 'GSVA', 'hexbin', 'hms', 'htmltools', 'httpuv',
  'knitr', 'leiden', 'libcoin', 'maftools', 'magick',
  'MatrixGenerics', 'matrixStats', 'memoise',
  'pairwiseComparisons', 'parallelly', 'performance', 'plotly',
  'quantreg', 'R.devices', 'rappdirs', 'Rcpp', 'RcppArmadillo',
  'reprex', 'rlang', 'RSQLite', 'rtracklayer', 'Seurat',
  'shiny', 'sp', 'spatstat.utils', 'systemfonts', 'tibble',
  'tinytex', 'withr', 'xfun'
Update all/some/none? [a/s/n]: if(!require(BSgenome.Hsapiens.UCSC.hg38))BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
Update all/some/none? [a/s/n]: 
Update all/some/none? [a/s/n]: 
Update all/some/none? [a/s/n]: #https://mirrors.ustc.edu.cn/bioc//packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.3.tar.gz
Update all/some/none? [a/s/n]: #如果多次下载都不成功，就下载tar.gz并放在工作目录下，本地安装
Update all/some/none? [a/s/n]: #install.packages("BSgenome.Hsapiens.UCSC.hg38_1.4.3.tar.gz",repos = NULL)
Update all/some/none? [a/s/n]: 
n
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  不存在叫‘BSgenome’这个名字的程辑包
**安装失败**

2.第二次安装

过程如下

> options("repos"="https://mirrors.ustc.edu.cn/CRAN/")
> if(!require("BiocManager")) install.packages("BiocManager",update = F,ask = F)
> options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/")
> if(!require(BSgenome))BiocManager::install("BSgenome")
载入需要的程辑包：BSgenome
载入需要的程辑包：BiocGenerics
载入需要的程辑包：parallel

载入程辑包：‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall,
    clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    anyDuplicated, 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

载入需要的程辑包：S4Vectors
载入需要的程辑包：stats4

载入程辑包：‘S4Vectors’

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

    expand.grid

载入需要的程辑包：IRanges

载入程辑包：‘IRanges’

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

    windows

载入需要的程辑包：GenomeInfoDb
载入需要的程辑包：GenomicRanges
载入需要的程辑包：Biostrings
载入需要的程辑包：XVector

载入程辑包：‘Biostrings’

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

    strsplit

载入需要的程辑包：rtracklayer
> if(!require(BSgenome.Hsapiens.UCSC.hg38))BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
载入需要的程辑包：BSgenome.Hsapiens.UCSC.hg38
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3
  (2020-10-10)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg38'
installing the source package ‘BSgenome.Hsapiens.UCSC.hg38’

试开URL’https://mirrors.ustc.edu.cn/bioc//packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.3.tar.gz'
Content type 'application/octet-stream' length 721596676 bytes (688.2 MB)
downloaded 688.2 MB

* installing *source* package 'BSgenome.Hsapiens.UCSC.hg38' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome.Hsapiens.UCSC.hg38'
    finding HTML links ... 好了
    package                                 html  
Rd warning: C:/Users/zzu/AppData/Local/Temp/RtmpsLa2AK/R.INSTALL4b81ae369d7/BSgenome.Hsapiens.UCSC.hg38/man/package.Rd:33: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/zzu/AppData/Local/Temp/RtmpsLa2AK/R.INSTALL4b81ae369d7/BSgenome.Hsapiens.UCSC.hg38/man/package.Rd:36: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.Hsapiens.UCSC.hg38)

The downloaded source packages are in
    ‘C:\Users\zzu\AppData\Local\Temp\RtmpgtI2Si\downloaded_packages’
Installation path not writeable, unable to update packages:
  boot, class, codetools, foreign, KernSmooth, Matrix, nlme,
  nnet, spatial
Old packages: 'backports', 'BH', 'brio', 'broom', 'caTools',
  'cli', 'coin', 'cpp11', 'crayon', 'crosstalk', 'data.table',
  'DBI', 'dbplyr', 'DelayedArray', 'deldir', 'diffobj', 'dplyr',
  'DT', 'edgeR', 'enrichplot', 'fansi', 'fastmap', 'findpython',
  'flextable', 'forcats', 'future.apply', 'gert', 'ggrepel',
  'ggridges', 'GSVA', 'hexbin', 'hms', 'htmltools', 'httpuv',
  'knitr', 'leiden', 'libcoin', 'maftools', 'magick',
  'MatrixGenerics', 'matrixStats', 'memoise',
  'pairwiseComparisons', 'parallelly', 'performance', 'plotly',
  'quantreg', 'R.devices', 'rappdirs', 'Rcpp', 'RcppArmadillo',
  'reprex', 'rlang', 'RSQLite', 'rtracklayer', 'Seurat',
  'shiny', 'sp', 'spatstat.utils', 'systemfonts', 'tibble',
  'tinytex', 'withr', 'xfun'
Update all/some/none? [a/s/n]: 
n
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  不存在叫‘BSgenome.Hsapiens.UCSC.hg38’这个名字的程辑包

再次安装失败

3. 将文件下载到本地安装

首先去https://mirrors.ustc.edu.cn/bioc//packages/3.12/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.3.tar.gz
下载文件，放到当前目录下。然后开始安装，过程如下：

> install.packages("BSgenome.Hsapiens.UCSC.hg38_1.4.3.tar.gz",repos = NULL)
Installing package into ‘C:/Users/zzu/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package 'BSgenome.Hsapiens.UCSC.hg38' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome.Hsapiens.UCSC.hg38'
    finding HTML links ... 好了
    package                                 html  
Rd warning: C:/Users/zzu/AppData/Local/Temp/RtmpuguyyM/R.INSTALL36d838247f33/BSgenome.Hsapiens.UCSC.hg38/man/package.Rd:33: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/zzu/AppData/Local/Temp/RtmpuguyyM/R.INSTALL36d838247f33/BSgenome.Hsapiens.UCSC.hg38/man/package.Rd:36: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.Hsapiens.UCSC.hg38)

安装成功！