请教R语言安装FlowCore未成功的相关问题

flowjo123

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。

niwanmao

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")

flowjo123

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。

flowjo123

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。

niwanmao

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

flowjo123

谢谢老师，逐步弄明白了R语言里的相关知识。