Sariya, Sanjeev
2018-Feb-01 16:23 UTC
[R] Error while working with png output on linux server
Thanks for your reply. I searched for the error on Google before resorting to the R forum (help group). I tried Sys.env(...) too, but didn't resolve the error I get. Hence I am looking for solution. -- -----Original Message----- From: Thierry Onkelinx [mailto:thierry.onkelinx at inbo.be] Sent: Thursday, February 01, 2018 10:57 AM To: Sariya, Sanjeev <ss5505 at cumc.columbia.edu> Cc: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>; r-help at r-project.org Subject: Re: [R] Error while working with png output on linux server Dear Sanjeev, It seems that you system neither supports X11 devices nor cairo devices. See http://lmgtfy.com/?q=R+unable+to+open+connection+to+X11 for possible solutions. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance thierry.onkelinx at inbo.be Havenlaan 88 bus 73, 1000 Brussel www.inbo.be /////////////////////////////////////////////////////////////////////////////////////////// To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey /////////////////////////////////////////////////////////////////////////////////////////// 2018-02-01 16:18 GMT+01:00 Sariya, Sanjeev <ss5505 at cumc.columbia.edu>:> Thanks for pointing to FAQ: I tried with cairo (shared in commands), unfortunately didn't work. > > -- > Sanjeev Sariya > > > -----Original Message----- > From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] > Sent: Thursday, February 01, 2018 10:12 AM > To: r-help at r-project.org; Sariya, Sanjeev <ss5505 at cumc.columbia.edu>; > r-help at r-project.org > Subject: Re: [R] Error while working with png output on linux server > > FAQ 7.19? > > Also, read the Posting Guide, in particular about posting using plain text. > -- > Sent from my phone. Please excuse my brevity. > > On February 1, 2018 6:50:42 AM PST, "Sariya, Sanjeev" <ss5505 at cumc.columbia.edu> wrote: >>I'm working on linux server: >>Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64 >>GNU/Linux >> >>I get error while creating png files. I'm sharing my commands and >>error while I run those commands: >> >>>png("abc", type="cairo") >>Error in .External2(C_X11, paste0("png::", filename), g$width, >>g$height, : >> unable to start device PNG >>In addition: Warning message: >>In png("abc", type = "cairo") : unable to open connection to X11 >>display '' >> >>> png("apoeqqplot.png", res=600) >>Error in .External2(C_X11, paste0("png::", filename), g$width, >>g$height, : >> unable to start device PNG >>In addition: Warning message: >>In png("apoeqqplot.png", res = 600) : >> unable to open connection to X11 display '' >> >>dev.off() >> >>R version 3.4.2 (2017-09-28) >>Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux >>9 (stretch) >> >>Matrix products: default >>BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so >>LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so >> >>locale: >>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>[7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>[9] LC_ADDRESS=C LC_TELEPHONE=C >>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >>attached base packages: >>[1] stats graphics grDevices utils datasets methods base >> >>other attached packages: >>[1] CMplot_3.3.1 >> >>loaded via a namespace (and not attached): >>[1] compiler_3.4.2 tools_3.4.2 >> >> >>How do I fix this? >> >> >> [[alternative HTML version deleted]] >> >>______________________________________________ >>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.
Henrik Bengtsson
2018-Feb-01 16:44 UTC
[R] Error while working with png output on linux server
You could try with png2() in the R.devices package, which is just a convenient wrapper around the bitmap() device which can also produce PNGs. It's not perfect but it might get you going. Henrik On Feb 1, 2018 08:24, "Sariya, Sanjeev" <ss5505 at cumc.columbia.edu> wrote:> Thanks for your reply. I searched for the error on Google before resorting > to the R forum (help group). > I tried Sys.env(...) too, but didn't resolve the error I get. Hence I am > looking for solution. > > > > -- > > > -----Original Message----- > From: Thierry Onkelinx [mailto:thierry.onkelinx at inbo.be] > Sent: Thursday, February 01, 2018 10:57 AM > To: Sariya, Sanjeev <ss5505 at cumc.columbia.edu> > Cc: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>; r-help at r-project.org > Subject: Re: [R] Error while working with png output on linux server > > Dear Sanjeev, > > It seems that you system neither supports X11 devices nor cairo devices. > See http://lmgtfy.com/?q=R+unable+to+open+connection+to+X11 > for possible solutions. > > Best regards, > > ir. Thierry Onkelinx > Statisticus / Statistician > > Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN > BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & > Kwaliteitszorg / Team Biometrics & Quality Assurance > thierry.onkelinx at inbo.be Havenlaan 88 bus 73, 1000 Brussel www.inbo.be > > //////////////////////////////////////////////////////////// > /////////////////////////////// > To call in the statistician after the experiment is done may be no more > than asking him to perform a post-mortem examination: he may be able to say > what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of > anecdote is not data. ~ Roger Brinner The combination of some data and an > aching desire for an answer does not ensure that a reasonable answer can be > extracted from a given body of data. ~ John Tukey > //////////////////////////////////////////////////////////// > /////////////////////////////// > > > > > 2018-02-01 16:18 GMT+01:00 Sariya, Sanjeev <ss5505 at cumc.columbia.edu>: > > Thanks for pointing to FAQ: I tried with cairo (shared in commands), > unfortunately didn't work. > > > > -- > > Sanjeev Sariya > > > > > > -----Original Message----- > > From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] > > Sent: Thursday, February 01, 2018 10:12 AM > > To: r-help at r-project.org; Sariya, Sanjeev <ss5505 at cumc.columbia.edu>; > > r-help at r-project.org > > Subject: Re: [R] Error while working with png output on linux server > > > > FAQ 7.19? > > > > Also, read the Posting Guide, in particular about posting using plain > text. > > -- > > Sent from my phone. Please excuse my brevity. > > > > On February 1, 2018 6:50:42 AM PST, "Sariya, Sanjeev" < > ss5505 at cumc.columbia.edu> wrote: > >>I'm working on linux server: > >>Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64 > >>GNU/Linux > >> > >>I get error while creating png files. I'm sharing my commands and > >>error while I run those commands: > >> > >>>png("abc", type="cairo") > >>Error in .External2(C_X11, paste0("png::", filename), g$width, > >>g$height, : > >> unable to start device PNG > >>In addition: Warning message: > >>In png("abc", type = "cairo") : unable to open connection to X11 > >>display '' > >> > >>> png("apoeqqplot.png", res=600) > >>Error in .External2(C_X11, paste0("png::", filename), g$width, > >>g$height, : > >> unable to start device PNG > >>In addition: Warning message: > >>In png("apoeqqplot.png", res = 600) : > >> unable to open connection to X11 display '' > >> > >>dev.off() > >> > >>R version 3.4.2 (2017-09-28) > >>Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux > >>9 (stretch) > >> > >>Matrix products: default > >>BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so > >>LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so > >> > >>locale: > >>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > >>[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > >>[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > >>[7] LC_PAPER=en_US.UTF-8 LC_NAME=C > >>[9] LC_ADDRESS=C LC_TELEPHONE=C > >>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >> > >>attached base packages: > >>[1] stats graphics grDevices utils datasets methods base > >> > >>other attached packages: > >>[1] CMplot_3.3.1 > >> > >>loaded via a namespace (and not attached): > >>[1] compiler_3.4.2 tools_3.4.2 > >> > >> > >>How do I fix this? > >> > >> > >> [[alternative HTML version deleted]] > >> > >>______________________________________________ > >>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 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. >[[alternative HTML version deleted]]
Jeff Newmiller
2018-Feb-01 17:09 UTC
[R] Error while working with png output on linux server
This is not an R issue so this is not a good venue... it has to do with which support software you have (not) installed. Try the R-sig-debian mailing list. Please clarify to them how you installed R... for Debian there are relevant deb packages and a corresponding Debian repository that provide the simplest route to a working system, but if you compile it yourself it is easy to miss dependencies. -- Sent from my phone. Please excuse my brevity. On February 1, 2018 8:23:13 AM PST, "Sariya, Sanjeev" <ss5505 at cumc.columbia.edu> wrote:>Thanks for your reply. I searched for the error on Google before >resorting to the R forum (help group). >I tried Sys.env(...) too, but didn't resolve the error I get. Hence I >am looking for solution. > > > >-- > > >-----Original Message----- >From: Thierry Onkelinx [mailto:thierry.onkelinx at inbo.be] >Sent: Thursday, February 01, 2018 10:57 AM >To: Sariya, Sanjeev <ss5505 at cumc.columbia.edu> >Cc: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>; r-help at r-project.org >Subject: Re: [R] Error while working with png output on linux server > >Dear Sanjeev, > >It seems that you system neither supports X11 devices nor cairo >devices. See http://lmgtfy.com/?q=R+unable+to+open+connection+to+X11 >for possible solutions. > >Best regards, > >ir. Thierry Onkelinx >Statisticus / Statistician > >Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN >BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie >& Kwaliteitszorg / Team Biometrics & Quality Assurance >thierry.onkelinx at inbo.be Havenlaan 88 bus 73, 1000 Brussel www.inbo.be > >/////////////////////////////////////////////////////////////////////////////////////////// >To call in the statistician after the experiment is done may be no more >than asking him to perform a post-mortem examination: he may be able to >say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural >of anecdote is not data. ~ Roger Brinner The combination of some data >and an aching desire for an answer does not ensure that a reasonable >answer can be extracted from a given body of data. ~ John Tukey >/////////////////////////////////////////////////////////////////////////////////////////// > > > > >2018-02-01 16:18 GMT+01:00 Sariya, Sanjeev <ss5505 at cumc.columbia.edu>: >> Thanks for pointing to FAQ: I tried with cairo (shared in commands), >unfortunately didn't work. >> >> -- >> Sanjeev Sariya >> >> >> -----Original Message----- >> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] >> Sent: Thursday, February 01, 2018 10:12 AM >> To: r-help at r-project.org; Sariya, Sanjeev <ss5505 at cumc.columbia.edu>; > >> r-help at r-project.org >> Subject: Re: [R] Error while working with png output on linux server >> >> FAQ 7.19? >> >> Also, read the Posting Guide, in particular about posting using plain >text. >> -- >> Sent from my phone. Please excuse my brevity. >> >> On February 1, 2018 6:50:42 AM PST, "Sariya, Sanjeev" ><ss5505 at cumc.columbia.edu> wrote: >>>I'm working on linux server: >>>Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64 >>>GNU/Linux >>> >>>I get error while creating png files. I'm sharing my commands and >>>error while I run those commands: >>> >>>>png("abc", type="cairo") >>>Error in .External2(C_X11, paste0("png::", filename), g$width, >>>g$height, : >>> unable to start device PNG >>>In addition: Warning message: >>>In png("abc", type = "cairo") : unable to open connection to X11 >>>display '' >>> >>>> png("apoeqqplot.png", res=600) >>>Error in .External2(C_X11, paste0("png::", filename), g$width, >>>g$height, : >>> unable to start device PNG >>>In addition: Warning message: >>>In png("apoeqqplot.png", res = 600) : >>> unable to open connection to X11 display '' >>> >>>dev.off() >>> >>>R version 3.4.2 (2017-09-28) >>>Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian >GNU/Linux >>>9 (stretch) >>> >>>Matrix products: default >>>BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so >>>LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so >>> >>>locale: >>>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>[7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>[9] LC_ADDRESS=C LC_TELEPHONE=C >>>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>>attached base packages: >>>[1] stats graphics grDevices utils datasets methods base >>> >>>other attached packages: >>>[1] CMplot_3.3.1 >>> >>>loaded via a namespace (and not attached): >>>[1] compiler_3.4.2 tools_3.4.2 >>> >>> >>>How do I fix this? >>> >>> >>> [[alternative HTML version deleted]] >>> >>>______________________________________________ >>>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.
Sariya, Sanjeev
2018-Feb-01 17:11 UTC
[R] Error while working with png output on linux server
Thank you. -- Sanjeev Sariya -----Original Message----- From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] Sent: Thursday, February 01, 2018 12:09 PM To: Sariya, Sanjeev <ss5505 at cumc.columbia.edu>; Thierry Onkelinx <thierry.onkelinx at inbo.be> Cc: r-help at r-project.org Subject: RE: [R] Error while working with png output on linux server This is not an R issue so this is not a good venue... it has to do with which support software you have (not) installed. Try the R-sig-debian mailing list. Please clarify to them how you installed R... for Debian there are relevant deb packages and a corresponding Debian repository that provide the simplest route to a working system, but if you compile it yourself it is easy to miss dependencies. -- Sent from my phone. Please excuse my brevity. On February 1, 2018 8:23:13 AM PST, "Sariya, Sanjeev" <ss5505 at cumc.columbia.edu> wrote:>Thanks for your reply. I searched for the error on Google before >resorting to the R forum (help group). >I tried Sys.env(...) too, but didn't resolve the error I get. Hence I >am looking for solution. > > > >-- > > >-----Original Message----- >From: Thierry Onkelinx [mailto:thierry.onkelinx at inbo.be] >Sent: Thursday, February 01, 2018 10:57 AM >To: Sariya, Sanjeev <ss5505 at cumc.columbia.edu> >Cc: Jeff Newmiller <jdnewmil at dcn.davis.ca.us>; r-help at r-project.org >Subject: Re: [R] Error while working with png output on linux server > >Dear Sanjeev, > >It seems that you system neither supports X11 devices nor cairo >devices. See http://lmgtfy.com/?q=R+unable+to+open+connection+to+X11 >for possible solutions. > >Best regards, > >ir. Thierry Onkelinx >Statisticus / Statistician > >Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN >BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie >& Kwaliteitszorg / Team Biometrics & Quality Assurance >thierry.onkelinx at inbo.be Havenlaan 88 bus 73, 1000 Brussel www.inbo.be > >/////////////////////////////////////////////////////////////////////// >//////////////////// To call in the statistician after the experiment >is done may be no more than asking him to perform a post-mortem >examination: he may be able to say what the experiment died of. ~ Sir >Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger >Brinner The combination of some data and an aching desire for an answer >does not ensure that a reasonable answer can be extracted from a given >body of data. ~ John Tukey >/////////////////////////////////////////////////////////////////////// >//////////////////// > > > > >2018-02-01 16:18 GMT+01:00 Sariya, Sanjeev <ss5505 at cumc.columbia.edu>: >> Thanks for pointing to FAQ: I tried with cairo (shared in commands), >unfortunately didn't work. >> >> -- >> Sanjeev Sariya >> >> >> -----Original Message----- >> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.ca.us] >> Sent: Thursday, February 01, 2018 10:12 AM >> To: r-help at r-project.org; Sariya, Sanjeev <ss5505 at cumc.columbia.edu>; > >> r-help at r-project.org >> Subject: Re: [R] Error while working with png output on linux server >> >> FAQ 7.19? >> >> Also, read the Posting Guide, in particular about posting using plain >text. >> -- >> Sent from my phone. Please excuse my brevity. >> >> On February 1, 2018 6:50:42 AM PST, "Sariya, Sanjeev" ><ss5505 at cumc.columbia.edu> wrote: >>>I'm working on linux server: >>>Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64 >>>GNU/Linux >>> >>>I get error while creating png files. I'm sharing my commands and >>>error while I run those commands: >>> >>>>png("abc", type="cairo") >>>Error in .External2(C_X11, paste0("png::", filename), g$width, >>>g$height, : >>> unable to start device PNG >>>In addition: Warning message: >>>In png("abc", type = "cairo") : unable to open connection to X11 >>>display '' >>> >>>> png("apoeqqplot.png", res=600) >>>Error in .External2(C_X11, paste0("png::", filename), g$width, >>>g$height, : >>> unable to start device PNG >>>In addition: Warning message: >>>In png("apoeqqplot.png", res = 600) : >>> unable to open connection to X11 display '' >>> >>>dev.off() >>> >>>R version 3.4.2 (2017-09-28) >>>Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian >GNU/Linux >>>9 (stretch) >>> >>>Matrix products: default >>>BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so >>>LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so >>> >>>locale: >>>[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>[7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>[9] LC_ADDRESS=C LC_TELEPHONE=C >>>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>>attached base packages: >>>[1] stats graphics grDevices utils datasets methods base >>> >>>other attached packages: >>>[1] CMplot_3.3.1 >>> >>>loaded via a namespace (and not attached): >>>[1] compiler_3.4.2 tools_3.4.2 >>> >>> >>>How do I fix this? >>> >>> >>> [[alternative HTML version deleted]] >>> >>>______________________________________________ >>>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.
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