Question: WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped'
gravatar for Razumall
5 months ago by
Razumall0 wrote:

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'

 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

[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     

ADD COMMENTlink modified 5 months ago by Peter Langfelder1.3k • written 5 months ago by Razumall0

This seems to be a bug, in the C code. Were you going through the tutorial?

ADD REPLYlink written 5 months ago by Lluís R300
gravatar for Peter Langfelder
5 months ago by
United States
Peter Langfelder1.3k wrote:

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.

ADD COMMENTlink written 5 months ago by Peter Langfelder1.3k
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