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我是 R 新手，正在尝试安装 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 )，但是安装包有困难。我的操作顺序如下：

  1. 安装 R（成功）

  2. 从 Hadley Wickham 安装“devtools”包（成功）

（输入以下命令）：

install.packages("devtools")
library(devtools)
  1. 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，我收到以下错误消息：

下载 github repo satijalab/seurat@master library.dynam(lib, package, package.lib) 中的错误：找不到共享对象'stringi.so'

...我已经查看了这个论坛以及谷歌来解决这个问题，但是，我没有太多的运气。任何帮助将不胜感激！

谢谢你，马克

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3 回答 3

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我刚刚用 cran 安装了 Seurant，没有错误。确保您运行的是 R 3.4 或更高版本。

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

在他们的网站上，他们只通过 github_install 安装预发布或开发版本。如果您还没有查看他们的网站，他们有一些很好的指导教程。

于 2018-11-09T19:29:03.817 回答
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从从未安装过的 R 中，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)
>

说到这里，您是否考虑过使用installed.packages()并remove.packages()手动删除（假定）以前版本的 seurat？

于 2015-08-03T19:36:26.220 回答
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几周前，我在两台 Debian 机器上安装了 SEURAT，我必须安装一些软件包才能使其正常工作：

gcc 4.9 至少
rJAVA
libssl-dev
plotutils

这些软件包必须安装在 R 之外（即使用 apt-get 或您在系统上使用的任何东西）。

于 2015-08-04T09:15:08.917 回答