[R] cannot open file '--no-restore.matrix'
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Sat Nov 23 19:13:23 CET 2019
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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