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
Related
I made a nice (aren't they all) app using VS 2013, debugged, tested etc. without much fuss and muss.
Now I want to pass it out to some friends for reality check, and so used the VS2015.Tools.Android.Publish Android App... feature.
I followed the instructions, got a Release build signed APK (and a non-signed APK too). I e-mailed the signed APK to myself on the Motorola Razr Turbo, and installed just fine.
However, it does not run. It just flashes up then terminates. I have reviewed the Xamarin instructions and tried a number of things but I am blocked for now. This app runs fine on the same phone after I have deployed it during development (Release build as well as Debug).
I feel I am missing something obvious to all those who have traveled this path before, and really would appreciate a pointer to a happier place.
Two things to check:
I often have to uninstall the previous version of the app (the one deployed during debugging/development).
Also, if the app requires some special permissions, check that those are still allowed.
Got it! Ah yes, have to run the old zipalign on the signed package. Help here (thanks Nigel) took me to use LogCat, and there was the problem. Found some more help at:
https://forums.xamarin.com/discussion/4169/apk-no-longer-working-on-device
and put together a batch file to run it; one line:
"C:\Users\mike\AppData\Local\Android\android-sdk\build-tools\23.0.3\zipalign.exe" -f -v 4 ./bin/Release/MyFineApp.SoNice-Signed.apk ./WillRunNow.apk
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.
I'm developing an application on two different machines (home and work) and while the home one seems to run just fine, the work one is, for lack of a better word, possessed. It has been exhibiting the following issues:
When loading the application, it will start at the simulator's main screen instead of starting the application at random intervals. You can start the application and have it work fine, then close the simulator, reload, and have the same codebase not load.
Going to applications doesn't show the application itself, in fact it never does.
Trying to load the applications cod file (File->load java program) never works. Tried the steps in this thread, with unreliable results.
Extremely small changes, such as modifying the value of a width variable by one, commenting out a function such as makeMenu or adding a button will cause code to no longer work, with no errors shown by the IDE.
Using clear.bat with sometimes work, sometimes not. Same with manually removing all files with the name of the project.
reinstalling the eclipse environment and the blackberry plugin did nothing more then burn off an hour.
having "load on startup" in the blackberry_app_descriptor.xml file is set.
Both systems are using Eclipse 3.5.1, BB plugin for eclipse 1.1 beta, Java 4.5 with the 8300 simulator. THe only difference that I am seeing is the operating system between the two systems. The work one being XP Sp3, home being vista. THe vista one isn't perfect, but I can test variable changes without flipping a coin to see if the app will even load or not.
I've tried the solutions that were similar on this forum, such as this one, but it looked to be that those solutions are dated as none of the options for the steps existed in my eclipse install.
So has anyone ran into such baffling behavior, and can it be fixed? Anything that I might have missed that could be tried?
I've been seeing this behavior with the new 1.1 plugin, the application doesn't load on startup and the FIle->load java program doesn't help. For me, the solution was I have to run a clean build every time, that is the eclipse clean and build instead of just build, not the clean.bat... Hope this helps!
Try clearing resources that have improper naming structure in your projects stuff with spaces or special character in the name of the file.
It took me two days to figure out.
One solution i got regarding your problem.
As I See Please run the application first time as Run as blackberry simulator
that is got start and here pick up run and then Run as Blackberry simulator