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Ana Marija

2019-Nov-23 18:21 UTC

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

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 at 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 at
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 at
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 at 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
at 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 at 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 at 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 at 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.
> >>>
> >>
>

Duncan Murdoch

2019-Nov-23 19:55 UTC

head link

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

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 at 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
at 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 at
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 at 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 at 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 at 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 at 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 at 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.
>>>>>
>>>>
>>

Henrik Bengtsson

2019-Nov-23 20:08 UTC

head link

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

Maybe it would help to add:

file<-paste(gene,"matrix",sep=".")
if (!file.exists(file)) stop("File not found: ", file)
filecluster<-read.table(file,header=T,sep=" ",dec=".")

/Henrik

On Sat, Nov 23, 2019 at 11:55 AM Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:>
> 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 at 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 at 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
at 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 at 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 at 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 at 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 at 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 at 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.
> >>>>>
> >>>>
> >>
>
> ______________________________________________
> R-help at 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.

R help - Nov 2019 - cannot open file '--no-restore.matrix'

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

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

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