[R] cannot open file '--no-restore.matrix'

Ana Marija @okov|c@@n@m@r|j@ @end|ng |rom gm@||@com
Sat Nov 23 17:05:19 CET 2019


Hi Ben,

I am not sure what you mean when you say to print, is it this?

> cmd_args=commandArgs(TRUE)
> print(cmd_args)
character(0)
> cmd_args=commandArgs()
> print(cmd_args)
[1] "/software/linux-el7-x86_64/compilers/r-3.6.1/lib64/R/bin/exec/R"

I changed in the first line of this script:
https://github.com/eleporcu/TWMR/blob/master/MR.R

cmd_args=commandArgs() to be cmd_args=commandArgs(TRUE)

but again I get the same error:

Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'NA.matrix': No such file or directory
Execution halted


Please advise,
Ana

On Sat, Nov 23, 2019 at 9:44 AM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> On 23/11/2019 10:26 a.m., Ana Marija wrote:
> > HI Ben,
> >
> > I tried it but it doesn't work:
> >
> > Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
> > Error in file(file, "rt") : cannot open the connection
> > Calls: read.table -> file
> > In addition: Warning message:
> > In file(file, "rt") :
> >    cannot open file '--no-restore.matrix': No such file or directory
> > Execution halted
> >
>
> You should print the cmd_args variable that is set on the first line of
> that script.  When I run a script that prints it using your command
> line, this is what it looks like:
>
> $ Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
> [1] "/Library/Frameworks/R.framework/Resources/bin/exec/R"
> [2] "--slave"
> [3] "--no-restore"
> [4] "--no-save"
> [5] "--file=MR.R"
> [6] "--args"
> [7] "ENSG00000154803.ld"
> [8] "ENSG00000154803.matrix"
>
> The next line
>
> gene <- cmd_args[3]
>
> is obviously wrong for my system, because it would set gene to
> "--no-restore".  Your results will probably be somewhat different, but
> it might be clear what you should use instead of the third element.
>
> By the way, changing the first line
>
> cmd_args=commandArgs()
>
> to
>
> cmd_args <- commandArgs(TRUE)
>
> makes a lot of sense in most cases.  I haven't read your whole script so
> I don't know it it makes sense for you.
>
> Duncan Murdoch
>
>
> > Please advise,
> > Ana
> >
> > On Sat, Nov 23, 2019 at 4:16 AM Ben Tupper <btupper using bigelow.org> wrote:
> >>
> >> Hi,
> >>
> >> I think you want this order...
> >>
> >> Rscript [options for R] script_file.R argument_1 argument_2 ...
> >>
> >> So, like this ...
> >>
> >> Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
> >>
> >> Cheers,
> >> Ben
> >>
> >> On Fri, Nov 22, 2019 at 8:59 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
> >>>
> >>> HI Ben,
> >>>
> >>> thank you so much , I did this:
> >>>
> >>> Rscript --no-save ENSG00000154803.ld ENSG00000154803.matrix  MR.R
> >>> Error: unexpected numeric constant in "1.000 0.089"
> >>> Execution halted
> >>>
> >>> I made ENSG00000154803.ld with:
> >>> library(MASS)
> >>> write.matrix(ENSG00000154803.ld, file="ENSG00000154803.ld")
> >>>
> >>> and it looks like this:
> >>>
> >>> 1.000 0.089 0.006 0.038 0.012 0.014 0.003 0.001 0.005 0.015 0.013
> >>> 0.000 0.000 0.000 0.001 0.003 0.000
> >>> 0.089 1.000 0.002 0.007 0.005 0.001 0.004 0.005 0.000 0.003 0.014
> >>> 0.001 0.012 0.005 0.000 0.004 0.004
> >>> 0.006 0.002 1.000 0.004 0.008 0.029 0.040 0.001 0.001 0.006 0.013
> >>> 0.054 0.006 0.002 0.010 0.001 0.000
> >>> 0.038 0.007 0.004 1.000 0.460 0.044 0.008 0.022 0.010 0.229 0.095
> >>> 0.066 0.010 0.030 0.001 0.003 0.000
> >>> 0.012 0.005 0.008 0.460 1.000 0.151 0.018 0.047 0.021 0.272 0.185
> >>> 0.002 0.003 0.066 0.006 0.004 0.004
> >>> 0.014 0.001 0.029 0.044 0.151 1.000 0.007 0.018 0.218 0.010 0.023
> >>> 0.016 0.000 0.025 0.000 0.005 0.000
> >>> 0.003 0.004 0.040 0.008 0.018 0.007 1.000 0.003 0.002 0.020 0.031
> >>> 0.128 0.019 0.005 0.030 0.002 0.016
> >>> 0.001 0.005 0.001 0.022 0.047 0.018 0.003 1.000 0.004 0.014 0.004
> >>> 0.098 0.010 0.012 0.001 0.006 0.003
> >>> 0.005 0.000 0.001 0.010 0.021 0.218 0.002 0.004 1.000 0.004 0.000
> >>> 0.012 0.000 0.006 0.018 0.004 0.013
> >>> 0.015 0.003 0.006 0.229 0.272 0.010 0.020 0.014 0.004 1.000 0.466
> >>> 0.001 0.091 0.057 0.062 0.002 0.005
> >>> 0.013 0.014 0.013 0.095 0.185 0.023 0.031 0.004 0.000 0.466 1.000
> >>> 0.238 0.180 0.073 0.058 0.000 0.006
> >>> 0.000 0.001 0.054 0.066 0.002 0.016 0.128 0.098 0.012 0.001 0.238
> >>> 1.000 0.158 0.006 0.044 0.006 0.001
> >>> 0.000 0.012 0.006 0.010 0.003 0.000 0.019 0.010 0.000 0.091 0.180
> >>> 0.158 1.000 0.077 0.237 0.009 0.000
> >>> 0.000 0.005 0.002 0.030 0.066 0.025 0.005 0.012 0.006 0.057 0.073
> >>> 0.006 0.077 1.000 0.056 0.000 0.004
> >>> 0.001 0.000 0.010 0.001 0.006 0.000 0.030 0.001 0.018 0.062 0.058
> >>> 0.044 0.237 0.056 1.000 0.000 0.003
> >>> 0.003 0.004 0.001 0.003 0.004 0.005 0.002 0.006 0.004 0.002 0.000
> >>> 0.006 0.009 0.000 0.000 1.000 0.002
> >>> 0.000 0.004 0.000 0.000 0.004 0.000 0.016 0.003 0.013 0.005 0.006
> >>> 0.001 0.000 0.004 0.003 0.002 1.000
> >>>
> >>> the other file (ENSG00000154803.matrix) looks like this:
> >>>
> >>> GENES ENSG00000154803 BETA_GWAS
> >>> rs12601631 -0.320577 -0.0160778
> >>> rs1708623 0.708706 0.0717719
> >>> rs1708628 -0.645996 -0.0973019
> >>> rs17804843 -0.78984 0.0059607
> >>> rs4078062 -0.340732 -0.0716837
> >>> rs4316813 -0.721137 -0.00502219
> >>> rs7217764 -0.61641 0.16997
> >>> rs7221842 -0.377727 -0.00184011
> >>> rs12602831 -0.397059 0.0154625
> >>> rs138437542 -0.590669 0.0145733
> >>> rs2174369 -0.167913 -0.0268728
> >>> rs242252 0.20184 0.0161709
> >>> rs34121330 0.328602 0.0753894
> >>> rs4792798 -0.303601 0.00227314
> >>> rs7222311 -0.367686 -0.0419168
> >>> rs74369938 0.687555 -0.223105
> >>> rs8075751 -0.261916 -0.0313484
> >>>
> >>> On Fri, Nov 22, 2019 at 7:44 PM Ben Tupper <btupper using bigelow.org> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> You might check the order of your arguments.   Options come before the
> >>>> script filename. See the details here...
> >>>>
> >>>> https://www.rdocumentation.org/packages/utils/versions/3.6.1/topics/Rscript
> >>>>
> >>>> Ben
> >>>>
> >>>> On Fri, Nov 22, 2019 at 8:17 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
> >>>>>
> >>>>> Hello,
> >>>>>
> >>>>> I am trying to run this code:
> >>>>> https://github.com/eleporcu/TWMR/blob/master/MR.R
> >>>>>
> >>>>> with r-3.6.1
> >>>>>
> >>>>> via:
> >>>>>
> >>>>> Rscript MR.R --no-save ENSG00000154803
> >>>>>
> >>>>> in the current directory I have saved: ENSG00000154803.ld and
> >>>>> ENSG00000154803.matrix as the software requires
> >>>>>
> >>>>> but I am getting this error:
> >>>>>
> >>>>> Error in file(file, "rt") : cannot open the connection
> >>>>> Calls: read.table -> file
> >>>>> In addition: Warning message:
> >>>>> In file(file, "rt") :
> >>>>>    cannot open file '--no-restore.matrix': No such file or directory
> >>>>> Execution halted
> >>>>>
> >>>>>
> >>>>> Please advise,
> >>>>>
> >>>>> Thanks
> >>>>> Ana
> >>>>>
> >>>>> ______________________________________________
> >>>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >>>>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> >>>>> and provide commented, minimal, self-contained, reproducible code.
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Ben Tupper
> >>>> Bigelow Laboratory for Ocean Science
> >>>> West Boothbay Harbor, Maine
> >>>> http://www.bigelow.org/
> >>>> https://eco.bigelow.org
> >>
> >>
> >>
> >> --
> >> Ben Tupper
> >> Bigelow Laboratory for Ocean Science
> >> West Boothbay Harbor, Maine
> >> http://www.bigelow.org/
> >> https://eco.bigelow.org
> >
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>



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