[BioC] FlowCore Question

[Mike]

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")
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> ​
>>>
>>
>


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