[R] cannot open file '--no-restore.matrix'
Ana Marija
@okov|c@@n@m@r|j@ @end|ng |rom gm@||@com
Sat Nov 23 19:21:30 CET 2019
Hi Duncan,
thanks, I just did,
Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
[1] "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
On Sat, Nov 23, 2019 at 12:13 PM Duncan Murdoch
<murdoch.duncan using gmail.com> wrote:
>
> On 23/11/2019 11:05 a.m., Ana Marija wrote:
> > 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
>
> You didn't put the print(cmd_args) into the script.
>
> Duncan Murdoch
> >
> >
> > 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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