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PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference
GNU Affero General Public License v3.0
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R crashes when I run tests/test_kernel.R #17

Closed brj1 closed 7 years ago

brj1 commented 7 years ago

I tried to build this package on my mac. I had to edit a few of the files since i installed igraph to /usr/local on my machine. I also had to remove the last parameter from igraph_neighborhood and igraph_neighborhood_size.

After I installed the Kaphi R pkg and ran the test.kernel.trivial() function in tests/test_kernel.R, R crashes with: caught segfault address 0x7fc7e5802c50, cause 'memory not mapped'

Traceback: 1: .Call("R_Kaphi_kernel", nwk1, nwk2, lambda, sigma, rho, normalize, PACKAGE = "Kaphi") 2: tree.kernel(t1, t1, lambda = 0.1, sigma = 2, rho = 1, normalize = 1, rescale.mode = "NONE") 3: test.kernel.trivial()

I wonder if it's an igraph version mismatch; I have version 0.7.1 of the igraph c library.

ArtPoon commented 7 years ago

Hi Brad,

Can you try pulling the submodule igraph with: git submodule update �init

Rosemary forked the igraph repo and made some changes, so to ensure version compatibility etc, it�s best to clone the one in the Kaphi repo.

Thanks!

On Nov 25, 2016, at 3:11 PM, Brad Jones notifications@github.com wrote:

I tried to build this package on my mac. I had to edit a few of the files since i installed igraph to /usr/local on my machine. I also had to remove the last parameter from igraph_neighborhood and igraph_neighborhood_size.

After I installed the Kaphi R pkg and ran the test.kernel.trivial() function in tests/test_kernel.R, R crashes with: caught segfault address 0x7fc7e5802c50, cause 'memory not mapped'

Traceback: 1: .Call("R_Kaphi_kernel", nwk1, nwk2, lambda, sigma, rho, normalize, PACKAGE = "Kaphi") 2: tree.kernel(t1, t1, lambda = 0.1, sigma = 2, rho = 1, normalize = 1, rescale.mode = "NONE") 3: test.kernel.trivial()

I wonder if it's an igraph version mismatch; I have version 0.7.1 of the igraph c library.

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brj1 commented 7 years ago

Ok, I got it working. I cloned Rosemary's repo into pkg/src/igraph. I then moved the repo back to where Rosemary forked it, since it wasn't working. I built and installed igraph and when i reinstalled Kaphi and ran the tests it worked.