Question: Error in systemPipeR
0
gravatar for Parham
4.3 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

Hi,

I am trying systemPipeR manual. In the very beginning I get following error. I don't know what to do. Any help is appreciated. 

Thanks!

> source("systemPipeRNAseq_Fct.R")
Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file 'systemPipeRNAseq_Fct.R': No such file or direc

ADD COMMENTlink modified 4.3 years ago by RamRS21k • written 4.3 years ago by Parham1.4k
2
gravatar for RamRS
4.3 years ago by
RamRS21k
Houston, TX
RamRS21k wrote:

Looks like you might not have the R script in your working directory. You can setwd() to the dir that contains the script, or copy it over to your working directory and then try again.

Also, doesn't look like your line is in the manual here

ADD COMMENTlink modified 7 months ago • written 4.3 years ago by RamRS21k

It doesn't say where this script is placed! Therefore I have no clue how to set the directory to it or copy it!

It's from section 2.2. from this manual if you could have a look please. 

http://bioconductor.org/packages/release/bioc/vignettes/systemPipeR/inst/doc/systemPipeRNAseq.pdf

Thanks!

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by Parham1.4k
1

You don't need to do both library() and source(). Use the link I gave you to install systempipeR and then run library(), that should work.

The source() is only if you have any custom functions to load.

ADD REPLYlink modified 7 months ago • written 4.3 years ago by RamRS21k

Oh thanks! I was doing both, now I skip source(). 

ADD REPLYlink written 4.3 years ago by Parham1.4k
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