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

Duncan Murdoch murdoch@dunc@n @end|ng |rom gm@||@com
Sat Nov 23 20:55:22 CET 2019


On 23/11/2019 1:21 p.m., Ana Marija wrote:
> 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
> 
Your script works with the third element in the list of arguments, and 
there are only two.

Duncan Murdoch

> 
> 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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