R坑二：Warning: cannot remove prior

安装TxDb.Hsapiens.UCSC.hg19.knownGene包，报错...

> BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
Bioconductor version 3.8 (BiocManager 1.30.8), R 3.5.1 (2018-07-02)
Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene'
installing the source package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz'
Content type 'application/x-gzip' length 18669702 bytes (17.8 MB)
downloaded 17.8 MB

* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
Error: package or namespace load failed for 'AnnotationDbi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'digest'
Error : package 'AnnotationDbi' could not be loaded
ERROR: lazy loading failed for package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
* removing 'C:/Users/zhangdengwei/Documents/R/win-library/3.5/TxDb.Hsapiens.UCSC.hg19.knownGene'
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign,
  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, rpart, survival
Warning message:
In install.packages(...) :
  installation of package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ had non-zero exit status

提示没有包digest没有，安装...

> library("digest")
Error in library("digest") : 不存在叫‘digest’这个名字的程辑包
> BiocManager::install("digest")
Bioconductor version 3.8 (BiocManager 1.30.8), R 3.5.1 (2018-07-02)
Installing package(s) 'digest'

  There is a binary version available but the source version is later:
       binary source needs_compilation
digest 0.6.21 0.6.22              TRUE

  Binaries will be installed
trying URL 'https://cran.csiro.au/bin/windows/contrib/3.5/digest_0.6.21.zip'
Content type 'application/zip' length 237366 bytes (231 KB)
downloaded 231 KB

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

The downloaded binary packages are in
    C:\Users\zhangdengwei\AppData\Local\Temp\RtmpIDBXB0\downloaded_packages
Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign,
  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, rpart, survival

提示Warning: cannot remove prior installation of package ‘digest’，迷糊了，没有咋个说不能删除之前的包
查看下是否有之前的digest包，可以通过以下方式找到本地存放R包的位置

image.png
还是Tools -> Install Packages，找到目录，只有今天安装的一个包
image.png
删掉，重启Rstudio，再次测试

> library("digest")
Error in library("digest") : 不存在叫‘digest’这个名字的程辑包
> BiocManager::install("digest")
Bioconductor version 3.8 (BiocManager 1.30.8), ?BiocManager::install for help
Bioconductor version '3.8' is out-of-date; the current release version '3.9' is available with R version
  '3.6'; see https://bioconductor.org/install
Bioconductor version 3.8 (BiocManager 1.30.8), R 3.5.1 (2018-07-02)
Installing package(s) 'digest'

  There is a binary version available but the source version is later:
       binary source needs_compilation
digest 0.6.21 0.6.22              TRUE

  Binaries will be installed
trying URL 'https://cran.csiro.au/bin/windows/contrib/3.5/digest_0.6.21.zip'
Content type 'application/zip' length 237366 bytes (231 KB)
downloaded 231 KB

package ‘digest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\zhangdengwei\AppData\Local\Temp\RtmpiAHo7v\downloaded_packages
Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign,
  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, rpart, survival
Old packages: 'digest'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
       binary source needs_compilation
digest 0.6.21 0.6.22              TRUE

  Binaries will be installed
trying URL 'https://cran.csiro.au/bin/windows/contrib/3.5/digest_0.6.21.zip'
Content type 'application/zip' length 237366 bytes (231 KB)
downloaded 231 KB

package ‘digest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\zhangdengwei\AppData\Local\Temp\RtmpiAHo7v\downloaded_packages
> library("digest")
Warning message:
程辑包‘digest’是用R版本3.5.3 来建造的 

果然成功了，R真是谜一样的软件，再次安装

> BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
Bioconductor version 3.8 (BiocManager 1.30.8), R 3.5.1 (2018-07-02)
Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene'
installing the source package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz'
Content type 'application/x-gzip' length 18669702 bytes (17.8 MB)
downloaded 17.8 MB

* installing *source* package 'TxDb.Hsapiens.UCSC.hg19.knownGene' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
** help
*** installing help indices
  converting help for package 'TxDb.Hsapiens.UCSC.hg19.knownGene'
    finding HTML links ... 好了
    package                                 html  
** building package indices
** testing if installed package can be loaded
Warning: package 'GenomicFeatures' was built under R version 3.5.3
Warning: package 'GenomeInfoDb' was built under R version 3.5.2
* DONE (TxDb.Hsapiens.UCSC.hg19.knownGene)
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\zhangdengwei\AppData\Local\Temp\RtmpiAHo7v\downloaded_packages’
Installation path not writeable, unable to update packages: boot, class, cluster, codetools, foreign,
  KernSmooth, lattice, MASS, Matrix, mgcv, nlme, rpart, survival
Old packages: 'digest'
Update all/some/none? [a/s/n]: 
a

  There is a binary version available but the source version is later:
       binary source needs_compilation
digest 0.6.21 0.6.22              TRUE

  Binaries will be installed
Warning: package ‘digest’ is in use and will not be installed
> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
载入需要的程辑包：GenomicFeatures
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, colMeans, colnames, colSums, dirname,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, 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：AnnotationDbi
载入需要的程辑包：Biobase
Welcome to Bioconductor

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

Warning messages:
1: 程辑包‘GenomicFeatures’是用R版本3.5.3 来建造的 
2: 程辑包‘GenomeInfoDb’是用R版本3.5.2 来建造的 

成功...