8000 segFault error in getTCGA : 'memory not mapped' · Issue #6 · zhandong/TCGA2STAT · GitHub
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GokceOGUZ opened this issue Sep 14, 2017 · 0 comments
Open

segFault error in getTCGA : 'memory not mapped' #6

GokceOGUZ opened this issue Sep 14, 2017 · 0 comments

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@GokceOGUZ
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Hi,

I am working with R.3.4.1 and using my institutes server. However, when I want to use getTCGA, I am facing this error:

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:

Could you please help me solve this problem.

Thanks in advance,

Gokce

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
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