Biostar Beta. Not for public use.
Installation error CNVkit: could not find the executable 'Rscript'
0
Entering edit mode
12 months ago
F ♦ 3.4k
Iran

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 • 288 views
ADD COMMENTlink
1
Entering edit mode

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
0
Entering edit mode

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
1
Entering edit mode

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

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink
1
Entering edit mode

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
0
Entering edit mode

Sorry

(py3venv) [fi1d18@cyan01 ~]$ /home/local/software/R/3.5.1/bin/Rscript"
ADD REPLYlink
1
Entering edit mode

So use this R then.

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink
1
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1