R坑三：package ‘TxDb.Hsapiens.UCSC.

装包package ‘TxDb.Hsapiens.UCSC.hg38.knownGen

> BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGen")
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Bioconductor version '3.8' is out-of-date; the current release version '3.9' is available with R version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) 'TxDb.Hsapiens.UCSC.hg38.knownGen'
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\RtmpcVJR0h\downloaded_packages
Warning message:
package ‘TxDb.Hsapiens.UCSC.hg38.knownGen’ is not available (for R version 3.5.1)

报错，package ‘TxDb.Hsapiens.UCSC.hg38.knownGen’ is not available (for R version 3.5.1)，去官网查

发现需要的R是3.6，而我的R是3.5.1，版本不对，换老式方法安装

source("https://bioconductor.org/biocLite.R")
biocLite("TxDb.Hsapiens.UCSC.hg38.knownGen")

测试

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.8 (BiocInstaller 1.32.1), ?biocLite for help
> 
> biocLite(“TxDb.Hsapiens.UCSC.hg38.knownGene”) 
Error: unexpected input in "biocLite(?
> biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene") 
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.8 (BiocInstaller 1.32.1), R 3.5.1 (2018-07-02).
Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
installing the source package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31934087 bytes (30.5 MB)
downloaded 30.5 MB

* installing *source* package 'TxDb.Hsapiens.UCSC.hg38.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.hg38.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.hg38.knownGene)
In R CMD INSTALL

The downloaded source packages are in
    ‘C:\Users\zhangdengwei\AppData\Local\Temp\RtmpcVJR0h\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\RtmpcVJR0h\downloaded_packages
Warning message:
'biocLite' is deprecated.
Use 'BiocManager::install' instead.
See help("Deprecated") 
> library("TxDb.Hsapiens.UCSC.hg38.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 

果然成功了