cyREST problem

[Afiqah Aleng]

Hi,

I want to use cyREST, but my computer cannot connect Rstudio with Cytoscape. I tried to use System Checker Script, downloaded from http://www.cytoscape.org/troubleshooting.html. 

When I run the script, this message came out:

Does anyone know how to fix this issue?

Hope anyone can help me to solve this

Thanks in advance. 

Afiqah

[Ruth Isserlin]

Hi Afiqah, 

Is cytoscape open?  I think for cytoscape 3.3 on windows you need to launch cytoscape with -R 1234 in order to get cyrest to initiate (In cytoscape 3.4 this happens automatically)

from the Cytoscape directory run:

cytoscape.bat -R 1234

Ruth 

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[Barry Demchak]

Hi, Afiqah –

 

Ruth’s advice is excellent … please let us know how it works.

 

Meanwhile, the troubleshooting script indicates that the Cytoscape App store can’t be reached from your PC. This is a problem, but wouldn’t contribute to your current issue. When you ran the troubleshooting script, was your PC connected to the Internet? Can you use your browser to surf to apps.cytoscape.org? Inability to contact the store isn’t fatal, but it will stop you from getting announcements, new apps, and so on.

 

Thanks.

--

[Afiqah Aleng]

Thanks Ruth and Barry for help. I have changed Cytoscape 3.4.0 instead of using Cytoscape 3.3.0. and it works. But for the apps problem, I cannot connect Cytoscape to the apps. and when i surf to apps.cytoscape.org, it showed "this site can't be reached". Basically, why does this problem occur?

Thanks

Afiqah

On Wed, Sep 7, 2016 at 10:07 PM, Barry Demchak <idekerlab...@gmail.com> wrote:

Hi, Afiqah –

 

Ruth’s advice is excellent … please let us know how it works.

 

Meanwhile, the troubleshooting script indicates that the Cytoscape App store can’t be reached from your PC. This is a problem, but wouldn’t contribute to your current issue. When you ran the troubleshooting script, was your PC connected to the Internet? Can you use your browser to surf to apps.cytoscape.org? Inability to contact the store isn’t fatal, but it will stop you from getting announcements, new apps, and so on.

 

Thanks.

 

From: cytoscape-helpdesk@googlegroups.com [mailto:cytoscape-helpdesk@googlegroups.com] On Behalf Of Afiqah Aleng
Sent: Tuesday, September 06, 2016 8:24 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] cyREST problem

 

Hi,

 

I want to use cyREST, but my computer cannot connect Rstudio with Cytoscape. I tried to use System Checker Script, downloaded from http://www.cytoscape.org/troubleshooting.html. 

When I run the script, this message came out:

 

 

Does anyone know how to fix this issue?

 

Hope anyone can help me to solve this

 

Thanks in advance. 

 

Afiqah

 

 

 

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[Barry Demchak]

Hi, Afiqah --

Thanks for your patience.

The App Store was down this afternoon after an unpredicted hardware crash. We have been working to bring it back up. It seems to be up now. Would you mind trying again and letting us know how it works for you now??

Thanks, and sorry for the trouble.

On Wed, Sep 7, 2016 at 8:03 PM, Afiqah Aleng <afiqa...@gmail.com> wrote:

Thanks Ruth and Barry for help. I have changed Cytoscape 3.4.0 instead of using Cytoscape 3.3.0. and it works. But for the apps problem, I cannot connect Cytoscape to the apps. and when i surf to apps.cytoscape.org, it showed "this site can't be reached". Basically, why does this problem occur?

Thanks

Afiqah

On Wed, Sep 7, 2016 at 10:07 PM, Barry Demchak <idekerlab...@gmail.com> wrote:

Hi, Afiqah –

 

Ruth’s advice is excellent … please let us know how it works.

 

Meanwhile, the troubleshooting script indicates that the Cytoscape App store can’t be reached from your PC. This is a problem, but wouldn’t contribute to your current issue. When you ran the troubleshooting script, was your PC connected to the Internet? Can you use your browser to surf to apps.cytoscape.org? Inability to contact the store isn’t fatal, but it will stop you from getting announcements, new apps, and so on.

 

Thanks.

 

From: cytoscape-helpdesk@googlegroups.com [mailto:cytoscape-helpdesk@googlegroups.com] On Behalf Of Afiqah Aleng
Sent: Tuesday, September 06, 2016 8:24 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] cyREST problem

 

Hi,

 

I want to use cyREST, but my computer cannot connect Rstudio with Cytoscape. I tried to use System Checker Script, downloaded from http://www.cytoscape.org/troubleshooting.html. 

When I run the script, this message came out:

 

 

Does anyone know how to fix this issue?

 

Hope anyone can help me to solve this

 

Thanks in advance. 

 

Afiqah

 

 

 

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[Afiqah Aleng]

Hi Barry,

Thanks a lot for your response. I already tried to open the apps manager and surf to http://apps.cytoscape.org/. And it works right now. Thank you very much. I really appreciate it.

Afiqah

vvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
vvvvvvvvvvvvvvvvvvvvvvvvvvvv

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[Barry Demchak]

Excellent news! Best of luck!

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