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

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Sat Nov 23 16:44:41 CET 2019


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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