Cytoscape installation on mac os majave

[jieand...@gmail.com]

Hi, I wanted to install this cytoscape but I found that maybe the os version isn't compatitable., so is there any solution now?

[David Otasek]

Hello,

Is there any specific error message or condition that prevents you from installing?

It would also be helpful if you ran the System Checker Script here and shared the results with us.

Thanks,

David

On Sun, Oct 14, 2018 at 4:19 PM <jieand...@gmail.com> wrote:

Hi, I wanted to install this cytoscape but I found that maybe the os version isn't compatitable., so is there any solution now?

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/837007e1-a9be-4c58-be4f-f5e72d65e325%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Reed Liu]

Hello,

The wrong information is as below,

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.6.0

Your shell is zsh

Fail: This version of OS is not supported: 10.14

Please upgrade your system to 10.11 or newer.

Thanks,

Reed

You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CAGXvV6T%2Bhkb2fwi7r3tBGpw5byaHV1DuYukLL1ZiVdY0wPLQ-g%40mail.gmail.com.

[M.Z. Rogon]

These releases are a huge PIA... I'm trying to get 3.7 to install and failing hard.

I mean I know we're looking at free software initiative, and you can't account for all possible problems and configurations, but there should be a few people on this planet capable of testing on at least 3 different versions of Mac OS...

It doesn't install on 10.13.6 either.

Hangs on "I accept the agreement" and runs away with 14 gigs of my RAM ;O

It's like the second button you need to click when installing, I'm pretty sure anyone trying to test it would encounter the issue ;P

PS. Checker script on the page is for version 3.6

On Sunday, October 21, 2018 at 9:26:14 AM UTC+2, Reed Liu wrote:

Hello,

The wrong information is as below,

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.6.0

Your shell is zsh

Fail: This version of OS is not supported: 10.14

Please upgrade your system to 10.11 or newer.

Thanks,

Reed

On Tue, Oct 16, 2018 at 2:05 AM David Otasek <dotas...@gmail.com> wrote:

Hello,

Is there any specific error message or condition that prevents you from installing?

It would also be helpful if you ran the System Checker Script here and shared the results with us.

Thanks,

David

On Sun, Oct 14, 2018 at 4:19 PM <jieand...@gmail.com> wrote:

Hi, I wanted to install this cytoscape but I found that maybe the os version isn't compatitable., so is there any solution now?

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

[Brett Settle]

Hi,

I'm sorry to hear you are having trouble installing Cytoscape. I recently upgraded from Mac OS 10.13 to Mac OS 14 (Mojave) and was able to install 3.7.0 on both versions. Most of our developers work on Mac and have not experienced this issue. I'm very curious to know why your installer froze.

I have since updated the system requirements checker to check for 3.7.0 and added 10.14 to the allowed OSs, but there could be unforeseen issues. 

Thanks,

Brett

[M.Z. Rogon]

Hi Brett,

Thank you, I've tried a couple of times with a reboot in between, I'll run the test tomorrow and let you know.

Cheers

Matt

[M.Z. Rogon]

Well I'm getting a fail with the checker:

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.7.0
Your shell is bash
Fail: This version of OS is not supported: 10.13.6

Please upgrade your system to 10.11 or newer.

[M.Z. Rogon]

I've upgraded to 10.14 and the installer worked. There was no way to make it happen on 10.13.6

Cheers

Matt

On Wednesday, October 24, 2018 at 4:43:07 PM UTC+2, Brett Settle wrote:

[Reed Liu]

Hi Rogon,

Did you solve this problem? Mine is 10.14 but still frozen when activate the installation wizard 

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/837007e1-a9be-4c58-be4f-f5e72d65e325%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/a287d358-d846-4257-81a9-6f967282abb2%40googlegroups.com.

[Reed Liu]

And this is where I stuck, I just couldn't click the accept button

 

On Fri, Oct 26, 2018 at 4:44 PM M.Z. Rogon <zro...@gmail.com> wrote:

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/837007e1-a9be-4c58-be4f-f5e72d65e325%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/a287d358-d846-4257-81a9-6f967282abb2%40googlegroups.com.

[Richie Kao]

I am having similar issues. My older version of Cytoscape 3.6.1 was running OK. I tried to upgrade it to 3.7.0 on my MacOS 10.3.6. The install went through but it won't run at all. I used the Mac.sh to check my system and got the message:  

- Fail: No Oracle JDK found.  Please download and install Oracle JDK:

http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

So I went to the link, downloaded jdk-8u192-macosx-x64 and installed JDK.

After that,  I ran the Mac.sh again. Although I saw some improvement, there is still an error message: 

Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk1.8.0_192.jdk

Fail: Java is not reachable.

Try re-installing Java 8.

I found this thread and people are having issues with 10.13.6. Then I updated my OS to 10.14. But I am still having the same issues. After I run the Cytoscape 3.7.0, the app icon of Cytoscape will show up but just stay in the dock without doing anything. Any suggestions? Thanks.

 
 

[ufuk....@gmail.com]

Same here, sitting on 10.13.6 and installer gets stuck in eternity eating RAM and burning CPU.. Without any error message.

The compatibility shell script passes without any hiccups:

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.7.0
Your shell is bash

Compatible OS version found: 10.13
- Pass: OS Version = 10.13.6
- Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk
/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk
- Pass: Current Java Version = 1.8.0_191
- Pass: JAVA_HOME found: /Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Contents/Home
Checking connection to Cytoscape App Store...
5 packets transmitted, 5 packets received, 0.0% packet loss
Done! You are ready to run Cytoscape 3.7.0

On Friday, October 26, 2018 at 3:29:05 PM UTC+2, Reed Liu wrote:
> And this is where I stuck, I just couldn't click the accept button
>
>
>  
>
>

[Alex Pico]

Intersting. It installed on my 10.13.6 without issue:

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.7.0

Your shell is bash

Compatible OS version found: 10.13

 - Pass: OS Version = 10.13.6

 - Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk

 - Pass: Current Java Version = 1.8.0_181

JAVA_HOME is not set.

Regardless, glad that an upgrade fixes the issues for others.

 - Alex

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/3416e74a-965b-4f5d-9ee6-f1ea53fbe1cf%40googlegroups.com.

[ufuk....@gmail.com]

I just tried to install 3.7..1 and still no joy... :(

[Scooter Morris]

Hi,

   Sorry to here about your issues.  We're looking into it, but at this point, we haven't been able to reproduce these problems.  We see at least several issues in this thread:

1. Installer hangs.  Some people have been able to get past this by upgrading to 10.14.  Apparently, there are some 10.13.6 issues.
2. Installer completes, but Cytoscape doens't run.  In this case, it would be helpful if you could try running it from a shell, then run cytoscape.sh (from the install directory).  The information on the screen would be helpful for debugging purposes.

-- scooter

[Alex Pico]

One idea we wanted to test was how the installer works with a non-admin account on MacOS. Here's what I see:

Installation of 3.7.1 completes through the "Finish" dialog and closes, but I can't find the installed Cytoscape_v3.7.1 folder or files. The install wizard says it'll be installed in the Applications folders, but it is simply not there. So I can't run Cytoscape.

This was reproduced on macOS 10.10 and 10.13.6.

Using an account with admin rights, the installation completes and Cytoscape works fine on two of my machines. So, I still can't reproduce issue #1, but perhaps this is the same as #2?

1. Installer hangs.  Some people have been able to get past this by upgrading to 10.14.  Apparently, there are some 10.13.6 issues.
2. Installer completes, but Cytoscape doens't run.  In this case, it would be helpful if you could try running it from a shell, then run cytoscape.sh (from the install directory).  The information on the screen would be helpful for debugging purposes.

 - Alex

[Ufuk Kirik]

@Scooter I can't update to Mojave unfortunately since I have some other software installed that is not compatible with 10.14 yet. 

@Alex Interesting point, I am actually using a non-admin account on my mac (old habit since I was working as a system admin for a computer lab). Does the installer have any assumption of the user account being an admin account? Normally if an installer requires admin access it asks you to authenticate via a dialog. I see no such thing, it just hangs after the license agreement.

--

You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/b59edd8f-0730-4f44-8639-ed7355fa9e2c%40googlegroups.com.

[Alex Pico]

Worth trying if you’re able to grant admin rights to yourself. I did not see any notifications about admin access in the installation process either.

 - Alex

[Richie Kao]

./cytoscape.sh

karaf.base: /Applications/Cytoscape_v3.7.0/framework

JAVA_HOME: null

             _                                    

   ___ _   _| |_  ___  ___  ___  __ _ _ __   ___  

  / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \ 

 | (__| |_| | |_| (_) \__ \ (__| (_| | |_) |  __/ 

  \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___| 

       |___/                         |_|          

Cytoscape 3.7.0

Hit '<tab>' for a list of available commands

   and '[cmd] --help' for help on a specific command.

Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

karaf@Cytoscape 3.7.0()> SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

SLF4J: Defaulting to no-operation (NOP) logger implementation

SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

Starting MetScape ... Done.

GpmlReaderFactoryImpl

Loaded KeyPathwayMiner

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

SLF4J: Defaulting to no-operation (NOP) logger implementation

SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

*******************************  ClueGO v2.5.1 (built:1742  24.04.2018) started  ************************************

******************************* CluePedia v1.5.1 (built:1743  24.04.2018) started ***********************************

So I tried and it seems to at least launch Cytoscape (3.7.0) GUI successfully. I still see the error message below and i still could not run it via double clicking the Cytoscape icon. Any more suggestions? I am on macOS 10.14.2 and the useer I am using is an admin-account. Thanks. 

############# Cytoscape System Requirements Checker for Mac ##############

Target Cytoscape version: 3.7.0

Your shell is bash

Compatible OS version found: 10.14

 - Pass: OS Version = 10.14.2

 - Pass: Following Oracle JDK found:

/Library/Java/JavaVirtualMachines/jdk1.8.0_192.jdk

/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk

Fail: Java is not reachable.

Try re-installing Java 8.

[ycha...@gmail.com]

The same problem here on Mojave. please help:

> /Library/Java/JavaVirtualMachines/jdk1.8.0_201.jdk
>
> /Library/Java/JavaVirtualMachines/jdk1.8.0_202.jdk

[marcel.g...@gmail.com]

SOLUTION TO STALLED INSTALLATION: Although the original post was some time ago, I also just ran into the same problem (setup stalls at license agreement) trying to install Cytoscape on MacOSX Mojave. I was able to solve the problem by turning off Magnet, a window placement app that is in wide use on MacOSX, and rerunning the installer. Just a side note, Magnet also messes with the operation of Matlab on MacOSX, so whatever it's doing it likely doesn't play nice with other apps as well. Too bad, because I love Magnet ;) So, perhaps this was the problem others were experiencing as well?

On Friday, October 26, 2018 at 8:29:05 AM UTC-5, Reed Liu wrote:
> And this is where I stuck, I just couldn't click the accept button
>
>
>  
>
>

[Scooter Morris]

Thanks!  Very useful information.

-- scooter

> To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

>
> To post to this group, send email to cytoscape...@googlegroups.com.
>
> Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
>
> To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/837007e1-a9be-4c58-be4f-f5e72d65e325%40googlegroups.com.
>
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
>
>
>
> --
>
> You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
>
> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.
>

> To unsubscribe from this group and all its topics, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

[bryantc...@gmail.com]

you are brilliant! Thank you .... it was magnet! thank you thank you thank you

[Ting Shi]

actually, I did not install magnet in Mac, but I still cannot install cytoscape3.7.1 on MacOSX mojave, it always hang on and I just couldn't click the accept button.

在 2019年5月14日星期二 UTC+8上午1:48:06，marcel....@gmail.com写道：

> To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

>
> To post to this group, send email to cytoscape...@googlegroups.com.
>
> Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
>
> To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/837007e1-a9be-4c58-be4f-f5e72d65e325%40googlegroups.com.
>
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
>
>
>
> --
>
> You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
>
> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.
>

> To unsubscribe from this group and all its topics, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

[Ting Shi]

Hi, did you solve your problem? I have the same problem and need your help, thank you so much.

在 2018年10月26日星期五 UTC+8下午9:29:05，Reed Liu写道：

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/837007e1-a9be-4c58-be4f-f5e72d65e325%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.

To unsubscribe from this group and all its topics, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

[Bryant A. Chambers]

Hey Ting Shi, 

I am no expert at cytoscape or much of anything at all. My issue was solved by disabling magnet. This is a small program that helps manage different windows in mac os. You say that you don’t have it. 

For what it is worth: you might look to see what additional programs you have running. Magnet seems to have had some overlap with Java control. Try disabling all of your extra software, anything you might be running in the background and ONLY run the installer. That might help. I believe there could be some conflicting software running. 

All the best,

Bryant

To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/22ecae46-207c-4272-8518-16a1270449cb%40googlegroups.com.

[morganv...@gmail.com]

Thank you SO MUCH for figuring this out!!!! LIFESAVER!!

> To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

>
> To post to this group, send email to cytoscape...@googlegroups.com.
>
> Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
>
> To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/837007e1-a9be-4c58-be4f-f5e72d65e325%40googlegroups.com.
>
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
>
>
>
> --
>
> You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
>
> To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/DUmJdEBvh0g/unsubscribe.
>

> To unsubscribe from this group and all its topics, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.