When I run Transitivity Clustering from clusterMaker2 in Cytoscape 3.8.2, it stops at the very beginning, and the task manager writes "Caught exception executing task".
It also happens when I try partitioning the network in the link below, where the Authors used TransClust for their work
http://www.plantphysiol.org/highwire/filestream/123923/field_highwire_adjunct_files/1/253807File_S3_FlowerNet_cytoscape_without_main_view.cys.zip
Any idea of what is happening?
Sorry! It's a bug that's been on my plate for fix for some time. There will be a new release of clusterMaker2 this summer and I'll make sure to fix it for that release.
-- scooter
Related
I'm new to Xamarin/Android, and so far it's been a pretty frustrating experience, compounded by code/AXML changes seemingly not being built or deployed to the emulator. I often find that a change I've just made seems to get ignored when I build and run the app.
My suspicions were confirmed when it started throwing an exception on a line in MainActivity.cs that I had commented out. Cleaning and rebuilding didn't help, and in the end deleted the bin and obj folders and uninstalled the app off the emulator for good measure (not sure which of these fixed it though).
Is it just me or is this a common issue? Is there anything I can do to prevent it from happening? I'm using VS2015 Community by the way.
Go to 'Tools/Configuration Manager' and make sure that both 'Build' and 'Deploy' options are checked for 'YourApp.Android' for active solution configuration and active solution platform. Then do 'Clean solution' and 'Rebuild solution', it should always work.
It looks like this is a common issue, as yet unresolved.
One of the comments in the above thread suggested that the problem can occur if you've only changed C# code, and unless you also "touch" one of the xml or axml files then the latest version won't be deployed. This seemed to do the trick in my case but it could have been a coincidence - Xamarin seems to be a temperamental beast, and will randomly fail to build or deploy on occasion, perhaps depending on the wind direction, or colour of my underwear that day.
I'm still in the early stages of learning Xamarin/Android, but if I don't enjoy the experience then I'll be jumping ship to Android Studio (although I'd prefer to stick with C# if I can).
I try example from ST for baseboard STM32F4DIS_BB + STM32F4-discovery.
I want to use RTOS example httpserver_socket. Before I use standalone (NO RTOS) httpserver example without problems. But in RTOS example the server was freeze on every web connection. It means that task are OK for LED toggle,DHCP is OK etc. Ping from CMD is OK. But when I make connection from web client the board was freezed and go to HardFault_Handler().
Any opinion?
Have you tried debugging the hard fault to see which instruction caused it? Once you know that you will be able to place a break point in the code to see how you got there.
As an aside, we have FreeRTOS+TCP running on an STM32F4 now, but on the larger eval board, rather than the Discovery board.
thanks to Richard. I found by debug and CFSR register that problem is in mem management :
"processor attempted an instruction fetch from a location that does
not permit execution. This fault occurs on any access to an XN region,
even when the MPU is disabled or not present"
But I dont understand how can ST make example for the same hardware what I have with this error? Now I try to find a problem.
I found that problem is in FPU option in project setting. Original project has set use FPU .When I set not used then project are OK. Problem in use of FPU and freeRTOS .
I am running plink software through a PBS batch job. This error occurs when I run the job:
*** glibc detected *** /software/plink: double free or corruption (out): 0x000000018dfafca0 ***
======= Backtrace: =========
[0x7d7691]
[0x7d8bea]
[0x45f5ed]
[0x47bb11]
[0x40669a]
[0x7bdb2c]
[0x400209]
However it only occur with one of my files (bw 30-60 gb files) and each rerun shows the exact same back trace map. I tried running it not through the batch scheduler and received the same error again, with the same backtrace map. I am just using the software (plink), and didn't write it, so most of the answers online are about writing and freeing memory in your program.
Any ideas on
what is causing this error, and
how I can fix it?
what is causing this error, and
A double-free or heap corruption in the plink
how I can fix it?
You can't. You can do one of two things, depending on how much you know and understand.
First, build the newest version of plink from source, and see if the problem persists.
If it does not, you are done (or at least you might hope that someone else found and fixed this problem).
If it does, you'll have to debug the problem sufficiently for either you, or plink developers to fix it. Some tools that should help: Valgrind and Address Sanitizer (note: in addition to Clang, Address Sanitizer is also included in GCC-4.8).
Once you have a good report (where the memory was allocated, and where it got corrupted), you should either fix it and submit your fix to plink developers, or give them a bug report with the allocation and corruption location and stack traces.
I'm starting with FreeRTOS and I'm trying to debug the Windows Demo. It compiles just fine but when I'm stepping in the code I can see that the assert inside the xTaskGenericCreate is being generated when FreeRTOS is trying to create the idle task.
I don't know why this is hapening since I haven't modified the original demo code.
Could anyone help me with this?
Regards
If you could say which assert was hit I could probably tell you right away what the issue is.
Is this the Windows project form the main FreeRTOS kernel download? Is it the Visual Studio or MingW/Eclipse version (https://www.freertos.org/FreeRTOS-Windows-Simulator-Emulator-for-Visual-Studio-and-Eclipse-MingW.html)? Did you make any changes at all, even if you think they are minor?
Is there any way to get the Dart2JS compiler to minimize time to output in any significant way? For example, is it possible to get it to compile only files which have been changed since the last compilation?
For context, I am experimenting with Dartangular. Compiling even a trivial hello world example takes 15-20 seconds, which in the long run becomes untenable to work with.
Recently dart2js had an issue which caused it to frequently run out of memory when to many tasks were run in parallel. To fix this issue they limited the number of tasks that can be run in parallel. This greatly slowed down the compilation speed but fixed the memory issue.
Development is usually done only in Dart and there is no compilation to JavaScript involved. This is mostly a deployment task. Of course it's also necessary to test the built result, so it is still important that it is fast.
As far as I know the Dart team is still working on it.
There is one option to increase heap size. and this will fix the run out of memory issue #Günter Zöchbauer mentioned,
--old_gen_heap_size=MEGABYTE_SIZE
For instance, --old_gen_heap_size=2048.
But i'm not quite sure this will speed up compilzation.