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[流式相关软件] 请教R语言安装FlowCore未成功的相关问题

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 楼主| 发表于 2021-10-12 09:50:28 | 显示全部楼层 |阅读模式
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1、最初用的R4.1.1,按照论坛之前的教程(https://www.flowcyto.cn/bbs/foru ... ;highlight=flowcore),在命令窗口依次输入下面两行命令:
source("http://bioconductor.org/biocLite.R"),显示R版本3.5及3.5以上去安装BiocManager

2、然后下载R3.4.2,输入source("http://bioconductor.org/biocLite.R"),提示选择储存library位置,选择好以后,显示package ‘BiocInstaller’ successfully unpacked and MD5 sums checked


安装成功。

3、输入biocLite("flowCore"),显示如下:


> biocLite("flowCore")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.2 (2017-09-28).
Installing package(s) ‘flowCore’
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  无法打开URL'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: dependencies ‘rrcov’, ‘corpcor’, ‘Rcpp’, ‘matrixStats’, ‘BH’ are not available
also installing the dependencies ‘Biobase’, ‘BiocGenerics’, ‘graph’


Warning: unable to access index for repository https://cran.rstudio.com/bin/windows/contrib/3.4:
  无法打开URL'https://cran.rstudio.com/bin/windows/contrib/3.4/PACKAGES'
试开URL’https://bioconductor.org/package ... /Biobase_2.38.0.zip
Error in download.file(url, destfile, method, mode = "wb", ...) :
  无法打开URL'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/Biobase_2.38.0.zip'
此外: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/Biobase_2.38.0.zip': HTTP status was '504 Gateway Time-out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘Biobase’ failed
试开URL’https://bioconductor.org/package ... Generics_0.24.0.zip
Error in download.file(url, destfile, method, mode = "wb", ...) :
  无法打开URL'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/BiocGenerics_0.24.0.zip'
此外: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/BiocGenerics_0.24.0.zip': HTTP status was '504 Gateway Time-out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘BiocGenerics’ failed
试开URL’https://bioconductor.org/package ... .4/graph_1.56.0.zip
Error in download.file(url, destfile, method, mode = "wb", ...) :
  无法打开URL'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/graph_1.56.0.zip'
此外: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/graph_1.56.0.zip': HTTP status was '504 Gateway Time-out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘graph’ failed
试开URL’https://bioconductor.org/package ... flowCore_1.44.2.zip
Error in download.file(url, destfile, method, mode = "wb", ...) :
  无法打开URL'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/flowCore_1.44.2.zip'
此外: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/flowCore_1.44.2.zip': HTTP status was '504 Gateway Time-out'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘flowCore’ failed
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  无法打开URL'https://cran.rstudio.com/src/contrib/PACKAGES'


未成功安装FlowCore,
1、请问各位老师有办法处理么?
2、如果安装新版的BiocManager,还有FlowCore么,如果没有,那还可以打开FCS文件么?
3、关于bioconductor开发的库的相关指令,在哪里可以查到呢?

小白不甚感激。

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发表于 2021-10-12 11:12:19 | 显示全部楼层
这是由于连接不上服务器的缘故。

改成国内清华大学的镜像:options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
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 楼主| 发表于 2021-10-12 11:45:43 | 显示全部楼层
niwanmao 发表于 2021-10-12 11:12
这是由于连接不上服务器的缘故。

改成国内清华大学的镜像:options(BioC_mirror="https://mirrors.tuna.ts ...

谢谢老师。
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 楼主| 发表于 2021-10-12 12:19:03 | 显示全部楼层
niwanmao 发表于 2021-10-12 11:12
这是由于连接不上服务器的缘故。

改成国内清华大学的镜像:options(BioC_mirror="https://mirrors.tuna.ts ...

你好老师,已安装好了,但似乎还是有部分没安装上。

我用教程里面的命令,试了各种方法,仍然未能打开FCS文件。你可以帮我看一下吗,谢谢老师。

1634012252.jpg
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发表于 2021-10-12 15:55:34 | 显示全部楼层
flowjo123 发表于 2021-10-12 12:19
你好老师,已安装好了,但似乎还是有部分没安装上。

我用教程里面的命令,试了各种方法,仍然未能打开FC ...

Rcpp包没安装好,所以你的flowCore应该是不完整的。
另外,读取FCS,函数是区分大小写的,应该是read.FCS
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 楼主| 发表于 2021-10-14 11:10:11 | 显示全部楼层
谢谢老师,逐步弄明白了R语言里的相关知识。
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