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gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
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Glmnet mex error on Windows 10 #3

Open agitter opened 5 years ago

agitter commented 5 years ago

Running SCINGE_Example on Windows 10 with MATLAB R2014b generated a system error: MATLAB has encountered an internal problem and needs to close.

The error details include the message Access violation detected. The first lines of the stack trace (with paths edited) are:

Stack Trace (from fault):
[  0] 0x00000000fe160b03 ...\MATLAB\R2014b\bin\win64\libmx.dll+00396035 MXGETPR+00000003
[  1] 0x00007ff879dc19dc ...\SCINGE\glmnet_matlab\glmnetMex.mexw64+00006620 MEXFUNCTION+00002524

Possibly related to these issues:

Re-compiling the Glmnet code may be the next step.

agitter commented 3 years ago

I tried running SINGE_Example on Windows 10 with MATLAB R2018a. It appears to run now. I'm still using the same version of glmnet_matlab I have from 2015 and did not recompile anything.

We should explore whether SINGE runs stably in Windows on newer versions of MATLAB.

Further testing shows that SINGE can run successfully in MATLAB R2018a on the example data (data1). The outputs match the reference outputs as well.

The aggregation step requires using Windows file separators \ in the path because of this line https://github.com/gitter-lab/SINGE/blob/49e34da529f5c639e23a5b7bc71a277ceab97988/code/SINGE_Aggregate.m#L18