MethylAid package visualize function not opening a web browser
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jdangelo • 0
@jdangelo-8953
Last seen 8.5 years ago
United States

Hi, 

I am currently trying to use the Bioconductor package, MethylAid. 

I am having problems with the visualize function. When called, following the example in section 2 (https://www.bioconductor.org/packages/release/bioc/vignettes/MethylAid/inst/doc/MethylAid.pdf, the web browser does not open a new window.

I was wondering if there is a url or another way to open the MethylAid interactive web application for your "summarized" idat files.

Please let me know if I need to add any other information about my issue.

Thanks,

Julian
illimina 450k methylation methyanalysis methylaid • 2.2k views
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More info on my issue:

The response to calling visualize(data) is the output:

The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
The 'clickId' argument is deprecated.  Please use 'click' instead.  See ?imageOutput or ?plotOutput for more information. (Last used in version 0.11.1)
Loading required package: shiny

Listening on http://XXXXXX

 

And then it hangs and never opens the methylaid interactive web application

 

Thanks,

Julian

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Sounds like maybe you are running R on a different machine (i.e. not the same machine on which you open the web browser)? I'm guessing this based on the fact that you elided the IP address, plus this is how an R session would behave if a shiny app was loaded on a remote machine (btw you can get back to your R prompt with control-c or with Escape if you are in RStudio).

What if you manually open a web browser and paste in the URL that is displayed (the one you render as http://XXXXXX)?

 

 

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Thank you for the response Dan,

What you are saying about running R on a different machine is definitely the case. I am running R through the terminal which is connected to a VM and I am trying to open us the web browser on my local computer.

I did indeed try to open up a web browser and use the URL displayed, but the page does not load.

 

Do you have any other suggestions?

 

Thanks,

Julian

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Is it a VM in the cloud? If so, you need to make sure that the port being used (the number after the last colon in the URL) is open to the outside (or at least to your IP address).

If R is telling you to connect to 127.0.0.1, you need to make a change. That is a special IP address that always refers to the machine itself, so if your VM is telling you to connect to 127.0.0.1 you can't do that from another machine.

If that is the case, you need to find out the IP address or host name of the VM, which should be straightforward because you probably used this to ssh to your VM. If the IP address is 1.2.3.4 you should enter this command in R:

options(shiny.host="1.2.3.4")

And then re-run the visualize() command. R will again tell you a URL where the shiny app can be found, paste this into your web browser.

 

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Thanks for the quick response again=)

I tried your solution and change shiny.host to my VM's IP address and re-ran the visualize command.

However, when I ran it, I got the following error:

Listening on http://1.2.3.4:XXXX
Error in startServer(host, port, handlerManager$createHttpuvApp()) :
  Failed to create serve

Then when I copied the  http://1.2.3.4:XXXX into a web browser, that page did not exist.

 

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1.2.3.4 is just an example. You need to use the actual IP address or host name of the vm.

I'm not sure how to tell you exactly how to find the IP address of your vm. It depends what kind of vm it is and how you are connected to it. If you are using Amazon EC2, you want to use the 'public dns name' of the machine.

Tell me what kind of vm you are using and how you are connected to it and I might be able to tell you how to find out its IP address or host name.

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jdangelo • 0
@jdangelo-8953
Last seen 8.5 years ago
United States

Sorry for the confusion, but I did NOT use 1.2.3.4 as the VM's IP. I used my actual VM's IP address. 

 

 
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Still need to know what kind of VM it is and how you connect to it.

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I used a VMware VM and connect to it through ssh with the VM's IP address through putty. 

Sorry I took so long to answer, my rating only allows a few posts every 6 hours.

Do you have any other suggestions?

Thanks again,

Julian

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Unfortunately I don't know much about VMware. Is the machine a guest on your local machine?

Or is it elsewhere on your network? You might need to contact your network administrator and ask them to open a port. Shiny will pick a random port each time but you can set the port to a specific number, say 5555, with:

options(shiny.port=5555)

Then you can ask your network admin to just open that port and try the visualize() command again. Let us know how it goes.

 

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To my understanding, VMWare is run as a hosted application through the local computer. I don't really know if it is a "guest" on my machine, but if it helps, I can access the mounted drive that is on the VM through my desktop. I also know that I have to use a vpn to connect to the school server before I can log onto the VM through it's IP address. 

 

Also, it isn't just the visualize function that doesn't open a web browser, but the browseVignettes command for any package also does not open up a web browser on it's own.

 

Open to any other suggestions as well.

 

Thanks,

Julian

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OK, this is helpful this tells me that the VM is located at your school and you are trying to access it from outside your school. So it is not a guest machine on your personal computer. 

It also suggests that your school's network is blocking the port (s)that you need in order to run browseVignettes() or visualize(). So my suggestion from before (that you contact a network admin) still holds. Alternatively, you could try and install R and methylAid on your personal computer and then you should not have any of these issues.

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Sorry for the late update, but in the end I was not able to get a port opened from support because of security issues (working through a hospital network server). What I ended up doing was to install RStudio on my local machine and install methylaid onto the local machine. Then I had to copy whatever files I want to run methylaid with onto my local machine. 

Thank you for the troubleshooting and support you provided Dan Tenenbaum

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