/usr/bin/env: Rscript: No such file or directory

[Samad Elka]

Hi, 

I'm trying first time to use ngs.plot.r on .bam file, I get the following error : /usr/bin/env: Rscript: No such file or directory

any suggestion ?

thanks in advance 

Samad

[ningyi shao]

Hi Samad,

You need put the path contains Rscript into your $PATH, something like this:

export PATH=$PATH;/your/R/path

Bests,

Ning-Yi

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[Samad Elka]

Hi Ning, 

Thank you, it working now!!

[archana bhardwaj]

I'm trying first time to use ngs.plot.r on . I get the following error : /usr/bin/env: Rscript: No such file or directory

As i set the path of R as export PATH=/path/R-2.8.1/bin/:$PATH in bashrc file

do i need to install some other version of R ( R 2.15) ??? 

waiting for reply 

 

[ningyi shao]

Your R is too old... I would suggest R 3.0 or above, as many ngs.plot dependent packages are not compatible to old R now.

Ning-Yi

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[Li Shen]

How about "which Rscript"? Does it show anything? 

Li

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Li Shen, Ph.D. Computer Science
Assistant Professor
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
New York, NY 10029
#################
ngs.plot - the coolest NGS plotting tool: https://code.google.com/p/ngsplot/

Want ChIP-seq differential analysis? Use: https://code.google.com/p/diffreps/

[archana bhardwaj]

I am trying to run ngs.plot.r from cygwin.  Then i set the environmental variables accordingly for R.3.2 , python 2.7.3 and NGSPLOT under .bashrc file.  There no problem with R and python during run using cygwin. if i called ngs.plot.r it  is showing.

Fatal error: cannot open file '/cygdrive/c/path/ngs_plot/ngsplot/bin/ngs.plot.r': No such file or directory 

please help me to solve this issue. 

waiting for reply

[Li Shen]

What if you run ngs.plot using the absolute path? For example, if you installed it under /path/to/ngsplot. You just type "/path/to/ngsplot/bin/ngs.plot.r" without quotes on console from any directory.

Li

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[archana bhardwaj]

Hello Li

I am calling ngs.plot.r in both way as 

1) $ ngs.plot.r

2) $  /cygdrive/c/Users/mnn/Desktop/ngs_plot/ngsplot/bin/ngs.plot.r

without any quotes... Still getting same error

Fatal error: cannot open file '/cygdrive/c/Users/mnn/Desktop/ngs_plot/ngsplot/bin/ngs.plot.r': No such file or directory

:(

[Li Shen]

Are they in your PATH? How about "which ngs.plot.r"?

Li

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