Question: Installation error CNVkit: could not find the executable 'Rscript'
0
gravatar for F
4 months ago by
F3.4k
Iran
F3.4k wrote:

Hi

I am not able to solve this error, any help please?

File "/home/fi1d18/.conda/envs/py3venv/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
RuntimeError: Could not find the executable 'Rscript' -- is it installed correctly?
(Original error: [Errno 2] No such file or directory: 'Rscript': 'Rscript')
make: *** [build/p2-5_5.cns] Error 1
(py3venv) [fi1d18@cyan02 test]$

I only know that my R is in this path

/local/software/R/3.5.1/bin/R

Also I have already installed DNAcopy r package

Thank you for any help

cnvkit • 320 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by F3.4k
1

https://github.com/etal/cnvkit/issues/111#issuecomment-221677565

The Rscript command is a binary that runs a given R script. It doesn't seem to be in your system path, but it's normally part of the default R installation, at least on Linux and R 3.0+. See if you can run Rscript independently on the command line, or locate it on your system.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax70k

Thanks a lot, I already installed that in

"/temp/hgig/fi1d18/cnvkit/scripts/DNAcopy/"

And inside that I have

(py3venv) [fi1d18@cyan01 cnvkit]$ ls
CITATION   cnvlib  devtools  docker  LICENSE     requirements.txt  setup.cfg  skgenome
cnvkit.py  data    doc       galaxy  README.rst  scripts           setup.py   test
(py3venv) [fi1d18@cyan01 cnvkit]$ cd scripts
(py3venv) [fi1d18@cyan01 scripts]$ ls
cnv_annotate.py              cnv_ztest.py    reference2targets.py
cnv_expression_correlate.py  DNAcopy         skg_convert.py
cnv_updater.py               guess_baits.py  snpfilter.sh
(py3venv) [fi1d18@cyan01 scripts]$ cd DNAcopy
(py3venv) [fi1d18@cyan01 DNAcopy]$ ls
benchmark  data  DESCRIPTION  help  INDEX  Meta       R
CHANGES    demo  doc          html  libs   NAMESPACE
ADD REPLYlink written 4 months ago by F3.4k
1

Looks like you installed R in your own space. Did Rscript not get installed when you did that?

ADD REPLYlink written 4 months ago by genomax70k

Sorry I only know library(DNAcopy) is available I am not sure how I can check the installation or location of Rscript :(

ADD REPLYlink written 4 months ago by F3.4k
1

Rscript is part of R install. Nothing to do with cnvkit.

Do you have R available on the system side (not one in your own directory)? Perhaps Rscript is available there.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax70k

Sorry

(py3venv) [fi1d18@cyan01 ~]$ /home/local/software/R/3.5.1/bin/Rscript"
ADD REPLYlink modified 4 months ago • written 4 months ago by F3.4k
1

So use this R then.

ADD REPLYlink written 4 months ago by genomax70k

How? I don't know how to tell software that this is my R

ADD REPLYlink written 4 months ago by F3.4k
1

When you do which Rscript or which R what do you see?

Remove /local/software/R/3.5.1/bin/ from your $PATH, if present.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax70k

Thanks a lot

Exactly by

 PATH=$(echo $PATH | sed -e 's;:\/local/software/R/3.5.1/bin/;;' -e 's/local/software/R/3.5.1/bin/:\?;;')

Likely software installed

Thank you for helping me

Very appreciated

ADD REPLYlink modified 4 months ago • written 4 months ago by F3.4k

Sorry, I was trying to install R package but I am getting this error

Warning in dir.create(lockdir, recursive = TRUE) :
  cannot create dir '/home/fi1d18/R/x86_64-pc-linux-gnu-library/3.5/00LOCK-NGScopy', reason 'Disk quota exceeded'
ERROR: failed to create lock directory '/home/fi1d18/R/x86_64-pc-linux-gnu-library/3.5/00LOCK-NGScopy'

How I can change directory to where I have more space like scratch/fi1d18 ?

ADD REPLYlink written 4 months ago by F3.4k

Please:

  1. Select a more descriptive title for your questions, e.g. Installation error CNVkit: could not find the executable 'Rscript'.
  2. Use tags appropriately. As such experts and developers can easily find your question. Tagging CNVkit would definitely make sense here, software error is useless.
  3. Take some time to read error messages carefully. In this case it is quite explicitly telling you what is wrong.
ADD REPLYlink written 4 months ago by WouterDeCoster40k
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