Monnie, Rob, No need to make this discussion private. Other BioC users might benefit from it. Cheers, H. Rob J Goedman wrote: > Hi Monnie, > > Can you try to start X11 (e.g. from the R Console). PNG needs X11 to > be running. > > Rob > > > On Aug 30, 2006, at 9:29 AM, McGee, Monnie wrote: > >> Dear Herve and Rob, >> >> I sent the following to the list, but, since you are the ones who >> answered my last Mac question, I thought you might be able to answer >> this one, too. >> >> Thanks, >> Monnie >> >> Monnie McGee, Ph.D. >> Assistant Professor >> Department of Statistical Science >> Southern Methodist University >> Ph: 214-768-2462 >> Fax: 214-768-4035 >> >> >> >> -----Original Message----- >> From: McGee, Monnie >> Sent: Wed 8/30/2006 11:27 AM >> To: bioconductor at stat.math.ethz.ch >> Subject: maQualityPlots on Mac >> >> Dear List, >> >> I am running R 2.3.1 on a Power Mac G5 with MAC OS 10.4.7 installed. >> I am running R from the Cocoa GUI. >> >> I tried using the package arrayQuality with the swirl zebrafish data, >> as outlined in the marray Quick start guide. I received the >> following error as I was working along: >> >>> maQualityPlots(mraw) >> Error in X11(paste("png::", filename, sep = ""), width, height, >> pointsize, : >> unable to start device PNG >> In addition: Warning message: >> unable to open connection to X11 display '' >> >> So I tried: >> >>> maQualityPlots(mraw,dev="jpeg") >> Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), >> width, : >> unable to start device JPEG >> In addition: Warning message: >> unable to open connection to X11 display '' >>> maQualityPlots(mraw,dev="ps") >> [1] "Format error, format will be set to PNG" >> Error in X11(paste("png::", filename, sep = ""), width, height, >> pointsize, : >> unable to start device PNG >> In addition: Warning message: >> unable to open connection to X11 display '' >>> maQualityPlots(mraw,dev="quartz") >> [1] "Format error, format will be set to PNG" >> Error in X11(paste("png::", filename, sep = ""), width, height, >> pointsize, : >> unable to start device PNG >> In addition: Warning message: >> unable to open connection to X11 display '' >>> >> >> Other graphics, like image() and plot(), run just fine. >> >> Incidentally, I tried running maQualityPlots using my X11 version of >> R, and the option dev="jpeg". I got the plots that I wanted. The >> function also ran with the default device (png), but my Mac could not >> open the files when I tried to display them. >> >> So, I have the devices on my computer ( at least, I have jpeg - but >> I'd like png, too. I think the quality would be better), but the GUI >> interface cannot find it. >> >> How do I get the correct device installed on my Mac and get the GUI >> to recognize it? >> >> Thanks, >> Monnie >> >> >> Monnie McGee, Ph.D. >> Assistant Professor >> Department of Statistical Science >> Southern Methodist University >> Ph: 214-768-2462 >> Fax: 214-768-4035 >> >> > -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Dear List, I am running R 2.3.1 on a Power Mac G5 with MAC OS 10.4.7 installed. I am running R from the Cocoa GUI. I tried using the package arrayQuality with the swirl zebrafish data, as outlined in the marray Quick start guide. I received the following error as I was working along: > maQualityPlots(mraw) Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : unable to start device PNG In addition: Warning message: unable to open connection to X11 display '' So I tried: > maQualityPlots(mraw,dev="jpeg") Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), width, : unable to start device JPEG In addition: Warning message: unable to open connection to X11 display '' > maQualityPlots(mraw,dev="ps") [1] "Format error, format will be set to PNG" Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : unable to start device PNG In addition: Warning message: unable to open connection to X11 display '' > maQualityPlots(mraw,dev="quartz") [1] "Format error, format will be set to PNG" Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : unable to start device PNG In addition: Warning message: unable to open connection to X11 display '' > Other graphics, like image() and plot(), run just fine. Incidentally, I tried running maQualityPlots using my X11 version of R, and the option dev="jpeg". I got the plots that I wanted. The function also ran with the default device (png), but my Mac could not open the files when I tried to display them. So, I have the devices on my computer ( at least, I have jpeg - but I'd like png, too. I think the quality would be better), but the GUI interface cannot find it. How do I get the correct device installed on my Mac and get the GUI to recognize it? Thanks, Monnie Monnie McGee, Ph.D. Assistant Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035

Have you installed the X11.app from the tiger/panther installation disks? The X11.app needs to be running in conjunction with R to then access the X11 graphics. I believe quartz() doesn't need X11.app to work. Also, I make a Rprofile.site file to store global options in R_HOME$/etc, For a system level install, it goes somewhere like; /Library/Frameworks/R.framework/Versions/Current/Resources/etc First <- function() { Sys.putenv("DISPLAY"=":0") # <----- this may be your problem too Sys.putenv("http_proxy"="http://[YOUR PROXY]:[PORT]") options(device="X11") } Marcus On 8/31/06 8:53 AM, "Herve Pages" <hpages at="" fhcrc.org=""> wrote: > Monnie, Rob, > > No need to make this discussion private. Other BioC users might benefit > from it. > Cheers, > > H. > > > Rob J Goedman wrote: >> Hi Monnie, >> >> Can you try to start X11 (e.g. from the R Console). PNG needs X11 to >> be running. >> >> Rob >> >> >> On Aug 30, 2006, at 9:29 AM, McGee, Monnie wrote: >> >>> Dear Herve and Rob, >>> >>> I sent the following to the list, but, since you are the ones who >>> answered my last Mac question, I thought you might be able to answer >>> this one, too. >>> >>> Thanks, >>> Monnie >>> >>> Monnie McGee, Ph.D. >>> Assistant Professor >>> Department of Statistical Science >>> Southern Methodist University >>> Ph: 214-768-2462 >>> Fax: 214-768-4035 >>> >>> >>> >>> -----Original Message----- >>> From: McGee, Monnie >>> Sent: Wed 8/30/2006 11:27 AM >>> To: bioconductor at stat.math.ethz.ch >>> Subject: maQualityPlots on Mac >>> >>> Dear List, >>> >>> I am running R 2.3.1 on a Power Mac G5 with MAC OS 10.4.7 installed. >>> I am running R from the Cocoa GUI. >>> >>> I tried using the package arrayQuality with the swirl zebrafish data, >>> as outlined in the marray Quick start guide. I received the >>> following error as I was working along: >>> >>>> maQualityPlots(mraw) >>> Error in X11(paste("png::", filename, sep = ""), width, height, >>> pointsize, : >>> unable to start device PNG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>> >>> So I tried: >>> >>>> maQualityPlots(mraw,dev="jpeg") >>> Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), >>> width, : >>> unable to start device JPEG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>>> maQualityPlots(mraw,dev="ps") >>> [1] "Format error, format will be set to PNG" >>> Error in X11(paste("png::", filename, sep = ""), width, height, >>> pointsize, : >>> unable to start device PNG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>>> maQualityPlots(mraw,dev="quartz") >>> [1] "Format error, format will be set to PNG" >>> Error in X11(paste("png::", filename, sep = ""), width, height, >>> pointsize, : >>> unable to start device PNG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>>> >>> >>> Other graphics, like image() and plot(), run just fine. >>> >>> Incidentally, I tried running maQualityPlots using my X11 version of >>> R, and the option dev="jpeg". I got the plots that I wanted. The >>> function also ran with the default device (png), but my Mac could not >>> open the files when I tried to display them. >>> >>> So, I have the devices on my computer ( at least, I have jpeg - but >>> I'd like png, too. I think the quality would be better), but the GUI >>> interface cannot find it. >>> >>> How do I get the correct device installed on my Mac and get the GUI >>> to recognize it? >>> >>> Thanks, >>> Monnie >>> >>> >>> Monnie McGee, Ph.D. >>> Assistant Professor >>> Department of Statistical Science >>> Southern Methodist University >>> Ph: 214-768-2462 >>> Fax: 214-768-4035 >>> >>> >> > ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}

Details on the second possibility, http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#TclTk-issues There was a typo in the function name, it is supposed to be '.First' . Marcus ----- Have you installed the X11.app from the tiger/panther installation disks? The X11.app needs to be running in conjunction with R to then access the X11 graphics. I believe quartz() doesn't need X11.app to work. Also, I make a Rprofile.site file to store global options in R_HOME$/etc, For a system level install, it goes somewhere like; /Library/Frameworks/R.framework/Versions/Current/Resources/etc First <- function() { Sys.putenv("DISPLAY"=":0") # <----- this may be your problem too Sys.putenv("http_proxy"="http://[YOUR PROXY]:[PORT]") options(device="X11") } Marcus On 8/31/06 8:53 AM, "Herve Pages" <hpages at="" fhcrc.org=""> wrote: > Monnie, Rob, > > No need to make this discussion private. Other BioC users might benefit > from it. > Cheers, > > H. > > > Rob J Goedman wrote: >> Hi Monnie, >> >> Can you try to start X11 (e.g. from the R Console). PNG needs X11 to >> be running. >> >> Rob >> >> >> On Aug 30, 2006, at 9:29 AM, McGee, Monnie wrote: >> >>> Dear Herve and Rob, >>> >>> I sent the following to the list, but, since you are the ones who >>> answered my last Mac question, I thought you might be able to answer >>> this one, too. >>> >>> Thanks, >>> Monnie >>> >>> Monnie McGee, Ph.D. >>> Assistant Professor >>> Department of Statistical Science >>> Southern Methodist University >>> Ph: 214-768-2462 >>> Fax: 214-768-4035 >>> >>> >>> >>> -----Original Message----- >>> From: McGee, Monnie >>> Sent: Wed 8/30/2006 11:27 AM >>> To: bioconductor at stat.math.ethz.ch >>> Subject: maQualityPlots on Mac >>> >>> Dear List, >>> >>> I am running R 2.3.1 on a Power Mac G5 with MAC OS 10.4.7 installed. >>> I am running R from the Cocoa GUI. >>> >>> I tried using the package arrayQuality with the swirl zebrafish data, >>> as outlined in the marray Quick start guide. I received the >>> following error as I was working along: >>> >>>> maQualityPlots(mraw) >>> Error in X11(paste("png::", filename, sep = ""), width, height, >>> pointsize, : >>> unable to start device PNG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>> >>> So I tried: >>> >>>> maQualityPlots(mraw,dev="jpeg") >>> Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), >>> width, : >>> unable to start device JPEG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>>> maQualityPlots(mraw,dev="ps") >>> [1] "Format error, format will be set to PNG" >>> Error in X11(paste("png::", filename, sep = ""), width, height, >>> pointsize, : >>> unable to start device PNG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>>> maQualityPlots(mraw,dev="quartz") >>> [1] "Format error, format will be set to PNG" >>> Error in X11(paste("png::", filename, sep = ""), width, height, >>> pointsize, : >>> unable to start device PNG >>> In addition: Warning message: >>> unable to open connection to X11 display '' >>>> >>> >>> Other graphics, like image() and plot(), run just fine. >>> >>> Incidentally, I tried running maQualityPlots using my X11 version of >>> R, and the option dev="jpeg". I got the plots that I wanted. The >>> function also ran with the default device (png), but my Mac could not >>> open the files when I tried to display them. >>> >>> So, I have the devices on my computer ( at least, I have jpeg - but >>> I'd like png, too. I think the quality would be better), but the GUI >>> interface cannot find it. >>> >>> How do I get the correct device installed on my Mac and get the GUI >>> to recognize it? >>> >>> Thanks, >>> Monnie >>> >>> >>> Monnie McGee, Ph.D. >>> Assistant Professor >>> Department of Statistical Science >>> Southern Methodist University >>> Ph: 214-768-2462 >>> Fax: 214-768-4035 >>> >>> >> > ______________________________________________________ The contents of this e-mail are privileged and/or confidenti...{{dropped}}