WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped'
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Razumall • 0
@razumall-11891
Last seen 7.5 years ago

Does anyone know about error message below after blockwiseModule().

> net = blockwiseModules(datExpr, power = 6,
+                        TOMType = "unsigned", minModuleSize = 30,
+                        reassignThreshold = 0, mergeCutHeight = 0.25,
+                        numericLabels = TRUE, pamRespectsDendro = FALSE,
+                        saveTOMs = TRUE,
+                        saveTOMFileBase = "femaleMouseTOM", 
+                        verbose = 3)
 Calculating module eigengenes block-wise fro

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: .Call("tomSimilarity_call", selExpr, as.integer(CcorType), as.integer(CnetworkType),     as.double(power), as.integer(CTOMType), as.integer(TOMDenomC),     as.double(maxPOutliers), as.double(quickCor), as.integer(fallback),     as.integer(cosineCorrelation), warn, as.integer(nThreads),     as.integer(callVerb), as.integer(callInd), PACKAGE = "WGCNA")
 2: blockwiseModules(datExpr, power = 6, TOMType = "unsigned", minModuleSize = 30,     reassignThreshold = 0, mergeCutHeight = 0.25, numericLabels = TRUE,     pamRespectsDendro = FALSE, saveTOMs = TRUE, saveTOMFileBase = "femaleMouseTOM",     verbose = 3)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

 

Attached the result of sessionInfo()

 

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  datasets  splines   utils     grDevices methods   base     

other attached packages:
[1] WGCNA_1.49            fastcluster_1.1.22    dynamicTreeCut_1.63-1 RcmdrMisc_1.0-5       sandwich_2.3-4       
[6] car_2.1-4     

wgcna • 1.5k views
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This seems to be a bug, in the C code. Were you going through the tutorial?

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@peter-langfelder-4469
Last seen 5 weeks ago
United States

Thanks for the bug report. It is difficult to say what the problem is apart from the obvious conclusion that it happens somewhere in the compiled code of WGCNA calculations. Try installing the newest WGCNA version and see if the problem persists.

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