I have successfully installed Cytoscape.
Version: 3.8.2
Java: 11.0.6 by AdoptOpenJDK
Java Home: /Applications/Cytoscape_v3.8.2/.install4j/jre.bundle/Contents/Home
OS: Mac OS X 10.15.6 - x86_64
I have successfully installed several apps.
However, only one of the apps JGF App shows in App drop down menu, none of the other apps seem present/active. For example, gexf-app should allow Cytoscape to import that format of file but neither 'File/Open' or 'File Import' recognize the file type.
Having read the docs, many file types are supported (seemingly) for import. However I have had no success in importing files which is arguably the most important to me at the moment.
How can I make the installed apps work or what may be preventing them from doing so?
Note: I this unanswered stackexchange question seems related.
Sorry to hear about your issues. My guess is that one of the apps you installed is crashing on startup and preventing the other apps from starting. I would start by disabling "JGF App" and "gexf-app" and see if the other apps all come up. Looking at the list of apps, you won't see them in the apps menu, though -- look in the tools menu for "Merge" and "Analyze Network". Then, you can enable gexf-app and see if it starts up (if it doesn't, you should see an indicator in the lower left-hand corner of Cytoscape). If you click it, it will give you a little more information about what happened. If that starts up fine, you can try to enable "JGF App".
-- scooter
Related
I have a question regarding Cytoscape. I just downloaded the newest version (v3.9.0) for Windows, but I am not able to open the actual application. Before I used v3.6.1 which ran perfectly fine, but I want to make use of the KEGGscape app which requires Cytoscape v3.8.0 or higher.
I have deleted the previous installation of Cytoscape, as well as made sure the cache was cleared. In addition, I downloaded the correct version of Java (Java version 11) and checked the system requirements with the script available on the website, which summarised: "Succes! You are ready to run Cytoscape 3.9.0."
So I am not exactly sure what I am missing and why it is not starting and hope anyone can help.
Thank you in advance.
Kind regards,
Sorry to hear you are having problems. When you say it doesn't start, does it correctly install, and the application doesn't start when you double-click it, or does the installer never start? If it's the former -- Cytoscape installs, but doesn't start, you could try opening up a console window and run cytoscape.bat from the directory that you installed it. That should give us more information about what the problem is. There should also be a file called framework-cytoscape.log in the CytoscapeConfiguration\3\ directory in your home. That will give us more information also.
-- scooter
Apologies in advance for the dated software question:
According to Code Composer help documentation the "Memory Load/Save Utility" should be be in the Tools menu. In my Code Composer 3.3 (which I have to use for this project, so I cannot upgrade), does not have this option in the tools menu, or any menu that I could find. It is not greyed out - it is just simply missing as far as I can tell. I've changed every view option to try and enable this.
Can anyone help me figure out how to enable/activate this option? Does the processor need to be in a specific state? Is this a special plug-in that I can't find?
Here is my setup:
Code Composer 3.3, Windows Xp, Using a Spectrum Digital xds510pp JTAG emulator on a TI ARM 9 processor.
Specifically the option is here: 13. Memory Load/Save Utility:
http://www.ti.com/lit/an/spraa07c/spraa07c.pdf
[EDIT] The File > Data > Save - this is not the same as the Memory Load/Save Utility. This sounds similar but does not export the values.
For example, I need to export data at a certain memory address for a certain length into a hex format.
Somehow my installation went bad.
I checked the Code Composer Studio Component Manager by running C:\CodeComposer3.3\cc\bin\comp_mgr.exe. Now, in this window un the TI node, there should be numerous plugins and one of which should be: "Memory Save/Load Utility Control..."
For me this was missing.
Repairing the installation via windows control panel did not work. I had to uninstall and then reinstalled. Upon reinstalling a TMS470 driver was reported missing. Not sure why this was.
Again, I uninstalled then complete removed the C:\CodeComposer3.3\ directory, then reinstalled. This time everything seemed to have worked and I do have the Memory Save/Load Utility and it is working.
EDIT:
It should also be noted that the plugins are bundled with the installer and could not be re installed separately.
I need to access the sandbox directory for an application installed on an iOS device, using the command line (non-gui) from a Mac or Linux. This is to help with development and testing automation. Dropping a json file into the sandbox lets me set parameters like extra debug messages and smaller refresh intervals.
A tool like iFunBox works perfectly but is graphical only, requiring numerous clicks to do this. Emails to the developers were unanswered. It also does not support AppleScript. I did find another app that provided a Fuse module, but it turned out buggy especially if the app was uninstalled and then reinstalled (in order to reset back to first time user experience). I reported the problems to the developer but there is no fix on the horizon.
The things I need to do are:
Test if an app with a specific bundle id is installed
Create Library/Caches/MYLIBNAME directory if it doesn't exist
Copy a ~100 byte json file from the Mac to that directory
Get a copy of that file
A solution that only works from Linux is acceptable too
Devices are not jailbroken and I would prefer not to need that as a requirement
In some cases I do not have the source code to the app since it is a third party using my library, so compiling different versions of the app isn't practical.
Answer is below in many comments thanks to lxt. Summary is:
Various libraries and programs associated with libimobiledevice can solve the problems
Use patched iFuse to mount an application sandbox
Use idevicesyslog to see the console log
Use ideviceinstaller to install/uninstall apps
The various libraries and programs associated with libimobiledevice are incredibly difficult if not impossible to compile as is on Linux or Mac, and there is no unified distribution of the source or binaries
For Ubuntu try libimobiledevice (may have 3 suffix), ideviceinstaller and libimobiledevice-utils packages
For Mac a search for libimobiledevice-macosx may get you some of the way there
This is going to be a little tricky, because as I think you've found out the application name is randomly generated on every install. I don't think there is a way past that, certainly that I know of. This explains the problems you're running into when simulating a new install (...the app directory name changes to a new, random hash, and then you're stuck).
Although my preference would be to access this config file in some other way (perhaps over a network, and have some code that only executes on debug/test builds check for it), if you did want to do this then I'd suggest trying something like writing a script that when you want to simulate a new install chooses the app directory that's most recently modified. But this is very hacky.
If you're not able to insert conditional code that only executes on debug/ test builds then I think the random app naming schema that iOS uses at a file system level is going to be problematic for you whatever approach you take.
Update: Regarding iFuse and libimobiledevice - out of the box it limits you to the documents directory. This is because the authors of iFuse don't entry-level users to be confused, and also because the structure is a little different depending on iOS version. You can comment out the lines in the iFuse source - fuse_opt_add_arg(&args, "-osubdir=Documents"); - to get access to the library directory through the mount. You will obviously need to re-compile iFuse yourself if doing this.
You can make use of MobileDevice Library
I know this is an old question and I doubt anyone is looking here anymore, but I thought I'd mention that you can use 'brew install libimobiledevice' to compile on the mac. There are a lot of dependencies and Homebrew really helps make it an easy process by installing them for you.
I am trying to use an application called CLUT.exe which is an old application for MS-DOS that can be used to reindex NTX files for DBF databases.
(This is not the main topic, but I am just writing this if someone wants to test the app and don't trust at all about the content).
The problem starts when trying to run the command line version through console (cmd.exe) and this error appears:
C:\>CLUT.exe [arg1] [arg2] [arg3]
run-time error R6009
- not enough space for environment
So, according to what I've searched, this could be a possible solution:
http://support.microsoft.com/default.aspx?scid=kb;en-us;230205
but it doesn't work and every alternative that I found to solve this over the internet is the same.
Another alternative could be to make right-click in the .exe file, go to Properties then Memory tab and increase the Initial environment memory from Auto to the max value but it doesn't work too.
Well, I am stuck and no "possible" solution is working for me. If someone is interested, knows more about this issue and want to test, you can download the application from here (click "Free Download" green button):
http://www.filebasket.com/free/Development-Clipper-programming-language/clut-exe/13996.html
or directly from my DropBox:
https://dl.dropbox.com/u/15208254/stackoverflow/clut_214.rar
Just to know, I am using Windows 7 and the CLUT.exe application is a Clipper based app (old programming language) that may run under windows console (cmd.exe).
Wikipedia does mention other dos emulators but, oddly, doesn't mention BOCHS.
Reindexing NTX files is not a difficult thing to do, and can be done with tools other than CLUT. For example, many of the utilities listed on this part of Download32 could be used. Otherwise, you could write your own using Harbour Project or xHarbour. Or contact me off list and I'll cook up something in Clipper 5.3.
LATER
If I read the README correctly for CLUT, it's a replacement for the DBU utility that comes with Clipper 5.x. I can supply you with a build of that if you're unsuccessful with other approaches.
Okay, I have been looking all over to solve this problem before I actually broke down and decided to finally ask for my psecific problem. I am using ClickOnce installation and when I use the setup.exe to install nothing runs, not even on my personal computer that I know has all of the proper libraries and such. I'm not sure what I am doing wrong so it is difficult to explain the problem.
I have included dotNetFramework4.0 client x86 x64 , xna redistributable 4.0 and windows installer 3.1 along with my game and I have it set to install all of that with setup , also I have it set to download prereqs from same location as application. I've tried it on three separate computers , one that does not have XNA or VS C# installed and the same problem occurs.
Here is the problem , after I install the game nothing runs, I try clicking on the ClickOnce application file (the one with my game's icon image) and again nothing happens. The thing that really bugs me is that there isn't any errors or crashes or anything , it's almost like clicking on the desktop screen. (I looked at the properties of the "shortcut" that was installed with the game and the file size of the shortcut is like 300 bytes. Isn't that really small? I was thinking maybe there is a problem with a startup executable? I'm not sure though.)
I've tried tweaking some stuff in the Publish section of my project , such as un-checking the box that says "use .deploy extension files" (I don't know why, I've been grasping at straws here) I've been looking into some other installers such as NSIS but I don't know how to compile a list of files to include in other installers and I feel like that won't solve the problem anyway because I've gotten ClickOnce to work with me before.
On one computer there was an error report that said something about 'deployment and application do not have matching security zones.'
Game.application resulted in exception. Following failure messages were detected:
+ Deployment and application do not have matching security zones.
It's getting late so if I need to provide more information let me know.
ClickOnce can be a fickle thing. There are times that I've had errors occur that could only be solved by recreating an entire Windows user profile. Because there are so many different options for ClickOnce, it's going to be hard for me to diagnose your exact issue, so I can only offer what options I used to successfully install via ClickOnce.
Publishing Folder: local folder
Installation Folder URL: blank
Install Mode: offline
Application Files
Make sure the Publish Status of your game files is set to Include (Auto)
Make sure the Publish Status of the XNA libraries is set to Prerequisite (Auto)
Click Prerequisites
Microsoft .NET Framework 4 Client Profile
Microsoft XNA Framework Redistributable 4.0
Windows Installer 3.1
Do not check for updates
Everything else default under Options (publisher/suite name shouldn't affect anything)
Specify the version number
Publish Now
Install the game through the setup.exe provided in the publish location. I always distribute every file that is publishes. However, you can clean up old versions in the "Application Files" folder if you don't want the history to be distributed.
You can double check the "Application Files" folder to see if your version got published correctly (look at the files that were deployed and see if they match your project contents).