Question

我是R的新手并试图安装Seurat来分析我的基因组单细胞数据。我想使用Seurat（http://www.satijalab.org/install.html），但是在安装软件包时遇到了困难。我的操作顺序如下：

安装R（成功）
安装＆＃34; devtools＆＃34;来自Hadley Wickham的包（成功）

（输入以下命令）：

install.packages("devtools")
library(devtools)

直接从Github安装Seurat（不成功）：

（尝试输入以下命令）：

install_github("satijalab/seurat")
library(Seurat)

...当我尝试从github安装Seurat时，收到以下错误消息：

正在下载github repo satijalab / seurat @ master library.dynam（lib，package，package.lib）中的错误：共享对象'stringi.so'未找到

...我已经看过这个论坛，以及谷歌，来解决这个问题，但是，我没有太多运气。任何帮助都会非常感激！

谢谢你，马克

Answer 1

从未安装过的seurat我可以证明您使用的代码是正确的。

> library(devtools)
> install_github("satijalab/seurat")
Downloading github repo satijalab/seurat@master
Installing Seurat
Installing 23 packages: ape, corpcor, DEoptimR, diptest, fastICA, flexmix, fpc, jackstraw, kernlab, lars, mclust, mixtools, modeltools, prabclus, robustbase, ROCR, Rtsne, segmented, trimcluster, tsne, useful, VGAM, XLConnectJars
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.rstudio.com/bin/windows/contrib/3.2/XLConnectJars_0.2-9.zip'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'The operation timed out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘XLConnectJars’ failed
package ‘ape’ successfully unpacked and MD5 sums checked
package ‘corpcor’ successfully unpacked and MD5 sums checked
package ‘DEoptimR’ successfully unpacked and MD5 sums checked
package ‘diptest’ successfully unpacked and MD5 sums checked
package ‘fastICA’ successfully unpacked and MD5 sums checked
package ‘flexmix’ successfully unpacked and MD5 sums checked
package ‘fpc’ successfully unpacked and MD5 sums checked
package ‘jackstraw’ successfully unpacked and MD5 sums checked
package ‘kernlab’ successfully unpacked and MD5 sums checked
package ‘lars’ successfully unpacked and MD5 sums checked
package ‘mclust’ successfully unpacked and MD5 sums checked
package ‘mixtools’ successfully unpacked and MD5 sums checked
package ‘modeltools’ successfully unpacked and MD5 sums checked
package ‘prabclus’ successfully unpacked and MD5 sums checked
package ‘robustbase’ successfully unpacked and MD5 sums checked
package ‘ROCR’ successfully unpacked and MD5 sums checked
package ‘Rtsne’ successfully unpacked and MD5 sums checked
package ‘segmented’ successfully unpacked and MD5 sums checked
package ‘trimcluster’ successfully unpacked and MD5 sums checked
package ‘tsne’ successfully unpacked and MD5 sums checked
package ‘useful’ successfully unpacked and MD5 sums checked
package ‘VGAM’ successfully unpacked and MD5 sums checked
"C:/PROGRA~1/R/R-32~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/Riorank/AppData/Local/Temp/RtmpSwBkRW/devtools200c34282ec7/satijalab-seurat-a0b8594"  \
  --library="C:/Program Files/R/R-3.2.1/library" --install-tests 

* installing *source* package 'Seurat' ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (Seurat)
>

有了这个，您是否考虑过使用installed.packages()和remove.packages()手动删除（假设）以前版本的seurat？

Answer 2

我几周前在两台Debian机器上安装了SEURAT，并且我必须安装包以使其正常工作：

gcc 4.9至少
rJAVA
中的libssl-dev的
plotutils

这些包必须安装在R之外（即使用apt-get或您在系统上使用的任何内容）。

Answer 3

我刚刚用Sranant安装了Seurant，没有任何错误。确保您正在运行R 3.4或更高版本。

install.packages('Seurat')
library(Seurat)

在他们的website上，他们仅通过github_install进行预发行或开发版本的安装。如果您还没有检查他们的网站，他们会提供一些不错的指导教程。

为单细胞基因组学安装Seurat-R工具包

3 个答案: