Great! On 09/09/2014 05:23 PM, michael wrote: > Hello Mike. > > I wanted to let you know that it is now working! I went ahead and > detached all the packages and restarted the server and no more problem. > > Great idea and thank you for your help. > > Michael > > On Sep 9, 2014, at 5:12 PM, Mike <wjiang2 at="" fhcrc.org=""> <mailto:wjiang2 at="" fhcrc.org="">> wrote: > >> So does `exprs` work now in the clean environment? >> >> On 09/09/2014 04:56 PM, michael wrote: >>> Hello Mike >>> >>> I made sure no other packages where loaded other than shiny and >>> shiny server running. I loaded flowCore. >>> >>> I get the following result when I check the class of dat. >>> >>> >>> > class(dat) >>> [1] "flowFrame" >>> attr(,"package") >>> [1] ?flowCore" >>> >>> >>> >>> On Sep 9, 2014, at 4:44 PM, Mike <wjiang2 at="" fhcrc.org="">>> <mailto:wjiang2 at="" fhcrc.org="">> wrote: >>> >>>> what does |class(dat)| return right after you |read.FCS|? Can you >>>> start a clean R session with only |flowCore| loaded to see if it >>>> works? I wonder if |exprs| method is somehow masked by other package. >>>> >>>> On 09/09/2014 04:35 PM, michael wrote: >>>> >>>> >>>> >>>>> Sorry that was the first issue I had. >>>>> >>>>> I upgraded to the newest version of flowCore and I no longer get >>>>> the RGL related error however I get this error when I load a file >>>>> using flowCore. >>>>> >>>>> dat <- read.FCS(?example.fcs", transformation=FALSE) >>>>> dat<-exprs(dat) >>>>> >>>>> >>>>> Error: unable to find an inherited method for function ?exprs? for >>>>> signature ?"table?? >>>>> >>>>> >>>>> >>>>> On Sep 9, 2014, at 4:17 PM, Mike <wjiang2 at="" fhcrc.org="">>>>> <mailto:wjiang2 at="" fhcrc.org="">> wrote: >>>>> >>>>>> What version are you using?The latest release `1.30.7` should >>>>>> already have fixed this issue. >>>>>> On 09/09/2014 04:05 PM, michael wrote: >>>>>>> Hello Mike, >>>>>>> >>>>>>> I am hoping to run flowCore on a headless server Amazon EC2 >>>>>>> using Ubuntu. I know one of the dependencies for flowCore is >>>>>>> RGL, however I get this message when flowCore tries to install RGL >>>>>>> >>>>>>> Warning in rgl.init(initValue, onlyNULL) : >>>>>>> RGL: unable to open X11 display >>>>>>> Warning in fun(libname, pkgname) : error in rgl_init >>>>>>> >>>>>>> I have been at this for a few days with no luck. Do you have >>>>>>> any experience with this? >>>>>>> >>>>>>> Many thanks >>>>>>> >>>>>>> Michael Kalnoky >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Jul 7, 2014, at 12:04 PM, Mike <wjiang2 at="" fhcrc.org="">>>>>>> <mailto:wjiang2 at="" fhcrc.org="">> wrote: >>>>>>> >>>>>>>> It is because one of the dependency package('rgl` or `ks`) >>>>>>>> failed to install. You have to tackle that before you can >>>>>>>> install flowCore. >>>>>>>> But if you install from the latest bioc release(2.14), you >>>>>>>> shouldn't have this problem since we've removed these >>>>>>>> dependencies since flowCore 1.30.7 >>>>>>>> On 07/07/2014 10:46 AM, michael wrote: >>>>>>>>> Hello Mike, >>>>>>>>> >>>>>>>>> Thank you for your quick reply. When I use these commands on >>>>>>>>> the Ubuntu server I receive the message below. I have >>>>>>>>> searched Stack Overflow to try and better understand what this >>>>>>>>> means. The package is not installing. >>>>>>>>> Do you have any ideas how this can be remedied? Thank you >>>>>>>>> very much for your time and help. >>>>>>>>> >>>>>>>>> Sincerely, >>>>>>>>> >>>>>>>>> Michael Kalnoky >>>>>>>>> >>>>>>>>> The downloaded source packages are in >>>>>>>>> ?/tmp/RtmpFCT8BO/downloaded_packages? >>>>>>>>> Updating HTML index of packages in '.Library' >>>>>>>>> Making 'packages.html' ... done >>>>>>>>> Warning messages: >>>>>>>>> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, >>>>>>>>> ...) : >>>>>>>>> installation of package ?rgl? had non-zero exit status >>>>>>>>> 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, >>>>>>>>> ...) : >>>>>>>>> installation of package ?ks? had non-zero exit status >>>>>>>>> 3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, >>>>>>>>> ...) : >>>>>>>>> installation of package ?feature? had non-zero exit status >>>>>>>>> 4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, >>>>>>>>> ...) : >>>>>>>>> installation of package ?flowCore? had non-zero exit status >>>>>>>>> >>>>>>>>> >>>>>>>>> On Jul 7, 2014, at 9:49 AM, Mike <wjiang2 at="" fhcrc.org="">>>>>>>>> <mailto:wjiang2 at="" fhcrc.org="">> wrote: >>>>>>>>> >>>>>>>>>> biocLite("flowCore") >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> ? >>> >> > [[alternative HTML version deleted]]