segFault error in getTCGA : 'memory not mapped'
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Entering edit mode
4.2 years ago
gokce.ouz ▴ 70

Hi All,

I wanted to use TCGA2STAT package to download Breast cancer data. However, I am facing the segfault error. I posted an issue on their github page. But they did not reply back to another user who raised the same issue last January. Therefore, could you please help me solve this problem?

Thanks in advance,

Gokce

P.s. : I am using the institute server and requested for 32 Gb so I think that should be enough memory, right ?

library(TCGA2STAT)
counts.brca <- getTCGA(disease="BRCA", data.type="RNASeq", type="count")

 *** caught segfault ***
address 0x3100000000, cause 'memory not mapped'

Traceback:
 1: .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks),     as.logical(replaceEntities), as.logical(asText), as.logical(trim),     as.logical(validate), as.logical(getDTD), as.logical(isURL),     as.logical(addAttributeNamespaces), as.logical(useInternalNodes),     as.logical(isHTML), as.logical(isSchema), as.logical(fullNamespaceInfo),     as.character(encoding), as.logical(useDotNames), xinclude,     error, addFinalizer, as.integer(options), as.logical(parentFirst),     PACKAGE = "XML")
 2: XML::htmlTreeParse("http://gdac.broadinstitute.org/runs/stddata__latest/",     useInternalNodes = T)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({    ldoc <- XML::htmlTreeParse("http://gdac.broadinstitute.org/runs/stddata__latest/",         useInternalNodes = T)}, error = function(e) {    ldoc = NULL})
 7: getTCGA(disease = "BRCA", data.type = "RNASeq", type = "count")

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


sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.5 (Final)

Matrix products: default
BLAS: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRblas.so
LAPACK: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] TCGA2STAT_1.2

loaded via a namespace (and not attached):
[1] compiler_3.4.1 XML_3.98-1.9
TCGA2STAT RNA-Seq BRCA R segfault • 3.3k views
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Entering edit mode

probably an issue of some version of a dependency package that was installed in binary version. So do not save the workspace. remove all the installed packages. restart the session or R or R studio whatever you are using, install TCGA2STAT again, load the library and try to run. It should be not a problem.Probably memory overload for the session or a package used having binary. Check this problem here.

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