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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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Errors while running ngsplot #64

Closed abhisheksinghnl closed 8 years ago

abhisheksinghnl commented 8 years ago

Hi,

I have installed ngsplot and also the associated genomes with it, along with it all the libraries.

The command that I use is

ngs.plot.r -G rn6 -R tss -C ChIPseq_input_banded_aortaM.sort.bam -O ngsaorta

the error that I get is 

Configuring variables...
Using database:
/home/6457/Softwares/ngsplot/database/rn6/rn6.ensembl.genebody.protein_coding.RData
Done
Loading R librariesA new version of Bioconductor is available after installing the most
  recent version of R; see http://bioconductor.org/install
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
Error in match(x, table, nomatch = 0L) : object 'ShortRead' not found
Calls: biocLite -> %in% -> match
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ShortRead’
Execution halted
You have new mail in /var/mail/root```

However, I have installed ShortRead library in R and it works well.

I am confused.

Please help.

Thank you