ggplot 2 issue [SOLVED]

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ggplot 2 issue [SOLVED]

Post by Clément Goubert on Tue Jan 05, 2016 11:38 am

Here is a little issue about ggplot2:

At present I meet a strange problem as following:

Code:
> library(ggplot2)
>
null device
          1
Error in library(ggplot2) : there is no package called ggplot2?
Execution halted
Done
Finishin time: Wed Sep  2 11:43:18 2015
########################
#   see you soon !!!   #
########################
hanminjin@micro:~/hmj/dnapipeTE/dnaPipeTE$



But I have successfully installed R (version 3.2.2) and ggplot2 package in the $Home passage.
I have tried, it runs very well, as fowlloing:


Code:
hanminjin@micro:~/hmj/dnapipeTE/dnaPipeTE$ R

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ggplot2)
> q()
Save workspace image? [y/n/c]: n


For ggplot2, could you tell me on what kind of machine you are running dnaPipeTE? Is it a clusters machine?
In my case, I have a file called .Renviron in my home folder on the calculus cluster in my lab. The path to my library are there and interpreted during the runs using this line of the file:

Code:
R_LIBS="/usr/remote/R_LIBS"

/usr/remote is the shared location of executable and libraries on my cluster.


Our machine is not a computer cluster.

OK so that is really strange that R cannot load ggplot2...
Try this in the dnaPipeTE folder:

Code:
Rscript ./landscapes.R ~/outfile/reads_landcapes ~/outfile/factors_and_colors

It should try to run only the R script to do the landscape graph


All problems have been solved.
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Clément Goubert
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