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. > >>> > >> >
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. >>>>> >>>> >>
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.