Question

在R 3.4.0上，我尝试安装DADA2。但它没有用......

> library("devtools")
> devtools::install_github("benjjneb/dada2")
Installation failed: Timeout was reached

所以我试过了（文件夹dada2-1.4在Tuto_DADA2中）（我先安装了Rtools 3.4.0）

> install.packages("~/Tuto_DADA2", repos = NULL, type = "source", dependencies = c("Depends", "Suggests","Imports"))
'\\CXXXW0001\Users\RXXXAn\Tuto_DADA2'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
'\\CXXXW0001\Users\RXXXAn\R\R-3.4.0' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
  running command '"//CXXXW0001/Users/RXXXAn/R/R-3.4.0/bin/x64/R" CMD INSTALL -l "\\CXXXW0001\Users\RXXXAn\R\R-3.4.0\library" "//CXXXW0001/Users/RXXXAn/Tuto_DADA2"' had status 1
Warning in install.packages :
  installation of package ‘//CXXXW0001/Users/RXXXAn/Tuto_DADA2’ had non-zero exit status

然后我试了

> install.packages("https://www.bioconductor.org/packages/release/bioc/src/contrib/dada2_1.4.0.tar.gz", repos = NULL, type="source")
trying URL 'https://www.bioconductor.org/packages/release/bioc/src/contrib/dada2_1.4.0.tar.gz'
Content type 'application/x-gzip' length 1709035 bytes (1.6 MB)
downloaded 1.6 MB

'\\CXXXW0001\Users\RXXXAn\Tuto_DADA2'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
'\\CXXXW0001\Users\RXXXAn\R\R-3.4.0' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
  running command '"//CXXXW0001/Users/RXXXAn/R/R-3.4.0/bin/x64/R" CMD INSTALL -l "\\CXXXW0001\Users\RXXXAn\R\R-3.4.0\library" "C:/Users/RXXXH~1/AppData/Local/Temp/RtmpGW3jsa/downloaded_packages/dada2_1.4.0.tar.gz"' had status 1
Warning in install.packages :
  installation of package ‘C:/Users/RXXXH~1/AppData/Local/Temp/RtmpGW3jsa/downloaded_packages/dada2_1.4.0.tar.gz’ had non-zero exit status

但是知道，我不知道该怎么做......

谢谢！

编辑：我不知道我做了什么，但安装有效，但加载软件包时出现错误消息...

> library(dada2)
Error: package or namespace load failed for ‘dada2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 aucun package nommé ‘GenomeInfoDbData’ n'est trouvé

当我尝试安装GenomeInfoDbData时：

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("GenomeInfoDbData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘GenomeInfoDbData’
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz'
Content type 'application/x-gzip' length 16238792 bytes (15.5 MB)
downloaded 15.5 MB

'\\CXXXW0001\Users\RXXXAn\Tuto_DADA2'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
'\\CXXXW0001\Users\RXXXAn\R\R-3.4.0' is not recognized as an internal or external command,
operable program or batch file.

The downloaded source packages are in
    ‘C:\Users\RXXXAn\AppData\Local\Temp\RtmpOqOI3E\downloaded_packages’
Old packages: 'DelayedArray', 'GenomeInfoDb', 'GenomicRanges', 'IRanges', 'S4Vectors', 'SummarizedExperiment', 'tibble'
Update all/some/none? [a/s/n]: 
n
Warning messages:
1: running command '"//CXXXW0001/Users/RXXXAn/R/R-3.4.0/bin/x64/R" CMD INSTALL -l "\\CXXXW0001\Users\RXXXAn\R\R-3.4.0\library" C:\Users\RXXXH~1\AppData\Local\Temp\RtmpOqOI3E/downloaded_packages/GenomeInfoDbData_0.99.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDbData’ had non-zero exit status

Answer 1

安装软件包的最简单方法几乎可以通过Bioconductor来处理，它可以处理所有依赖项管理并避免编译任何内容。

source("https://bioconductor.org/biocLite.R")
biocLite("dada2")

安装dada2不起作用

1 个答案: