安装Seurat -R单细胞基因组工具包
安装Seurat -R单细胞基因组工具包
提问于 2015-08-03 19:26:02
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。但是，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。我的行动顺序如下：
- 安装R(成功)
- 从Hadley Wickham安装"devtools“软件包(成功)
(输入以下命令)：
install.packages("devtools")
library(devtools)- 安装Seurat -直接从Github (不成功)：
(试图输入以下命令)：
install_github("satijalab/seurat")
library(Seurat)...When我试图从github安装Seurat，我收到以下错误消息：
下载library.dynam(lib，package，package.lib)中的/seurat@master错误:找不到共享对象‘stringi.so’
...I已经在这个论坛上，以及谷歌，来解决这个问题，然而，我没有太多的运气。任何帮助都是非常感谢的！
谢谢你，马克
回答 3
Stack Overflow用户
发布于 2018-11-09 19:29:03
我刚给Seurant安装了cran，没有错误。确保您运行的R3.4或更高。
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。如果你还没有检查他们的网站，他们有一些很好的指导教程。
Stack Overflow用户
发布于 2015-08-03 19:36:26
从一个从未安装过seurat的R中，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)
> 您考虑过使用installed.packages()和remove.packages()手动删除(假设)以前版本的seurat吗？
Stack Overflow用户
发布于 2015-08-04 09:15:08
几周前，我在两台Debian机器上安装了SEURAT，为了使它正常工作，我不得不安装一些软件包：
gcc 4.9
rJAVA
libssl-dev
倍体
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)。
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原文链接：
https://stackoverflow.com/questions/31795226
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