Question

motifStack crashes for example from documentation

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map2085 ▴ 40

@map2085-9227

Last seen 6.7 years ago

United States

motifStack crashes when trying to execute one of the examples from its own documentation (from page 5 of the vignette)

Namely, the following code exactly reproduces the crash:

pcms <- readPCM(file.path(find.package("motifStack"),"extdata"),"pcm$")

motifs <- lapply(pcms,pcm2pfm)

motifStack(motifs,layout="stack",ncex=1.0)

This causes R to segfault. Below if the error message produced by R

> motifStack(motifs,layout="stack",ncex=1.0)

*** caught segfault ***
address 0x3a00000000, 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: xmlTreeParse(rgmlFile, ...)
3: readPicture(paste(psfilename, ".xml", sep = ""))
4: coloredSymbols(ncha, font, colset, rname, fontsize)
5: plotMotifLogo(pfm = x@mat, motifName = x@name, p = x@background[rownames(x@mat)], colset = x@color[rownames(x@mat)], ...)
6: plot(pfms[[n - i + 1]], xlab = NA, ...)
7: plot(pfms[[n - i + 1]], xlab = NA, ...)
8: plotMotifLogoStack(pfms, ...)
9: motifStack(motifs, layout = "stack", ncex = 1)

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

motifstack • 2.3k views

ADD COMMENT • link updated 8.9 years ago by Ou, Jianhong ★ 1.3k • written 8.9 years ago by map2085 ▴ 40

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Hi,

I can't reproduce this. Your installation might be out-of-sync. Please show the output of:

library(motifStack)
sessionInfo()

Thanks,

H.

ADD REPLY • link 8.9 years ago Hervé Pagès 16k

score 0 · Answer 1 · 2016-02-11

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Ou, Jianhong ★ 1.3k

@ou-jianhong-4539

Last seen 12 days ago

United States

Hi,

Could you try code like this:

library(grImport)
tmp <- tempfile()
cat("%!PS\nnewpath\n0 0 moveto\n-5 10 lineto\n-10 20 10 20 5 10 curveto\n5 10 lineto\nclosepath\n0 setgray\nfill\n", file=tmp)
PostScriptTrace(tmp, outfile=paste0(tmp, ".xml"))
pic <- readPicture(paste0(tmp, ".xml"))
grid.picture(pic)

And let me know what happens.

ADD COMMENT • link 8.9 years ago Ou, Jianhong ★ 1.3k

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Hi, I installed ATACseqQC and met the same "* caught segfault *" problem. I traced to this post, tried this code. Here is the result.

BTW, the path of ghostscript has been set with Sys.setenv(RGSCMD="PATHTO_GS")

library(grImport)

Loading required package: grid

Loading required package: XML

tmp <- tempfile()

cat("%!PS\nnewpath\n0 0 moveto\n-5 10 lineto\n-10 20 10 20 5 10 curveto\n5 10 lineto\nclosepath\n0 setgray\nfill\n", file=tmp)

PostScriptTrace(tmp, outfile=paste0(tmp, ".xml"))

pic <- readPicture(paste0(tmp, ".xml"))

* caught segfault *

address 0x7fa900000000, cause 'memory not mapped'

Traceback:

1: xmlTreeParse(rgmlFile, ...)

2: readPicture(paste0(tmp, ".xml"))

Possible actions:

1: abort (with core dump, if enabled)

2: normal R exit

3: exit R without saving workspace

4: exit R saving workspace

ADD REPLY • link 5.8 years ago chenzixi07 • 0

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Hi chenzixi,

Thank you for confirm this segment fault agian. Could you try to re-install grImport from source like this:

install.packages("grImport", type="source")

and then re-run the code above. Before you run pic <- readPicture(paste0(tmp, ".xml")), could you please run sessionInfo() and send me your session info. So I can repeat your error.

Jianhong.

ADD REPLY • link 5.8 years ago Ou, Jianhong ★ 1.3k

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Hi Jianhong,

Thanks for your reply.

I re-install the grImport package as you suggested. Here is the sessionInfo.

>sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final)

Matrix products: default BLAS: /PUBLIC/software/RNA/R/R-3.5.1/lib64/R/lib/libRblas.so LAPACK: /PUBLIC/software/RNA/R/R-3.5.1/lib64/R/lib/libRlapack.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C
[3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LCPAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] grImport0.9-1.1 XML3.98-1.16

loaded via a namespace (and not attached): [1] compiler3.5.1 tools3.5.1

I also tried the motifStack script mentioned above, and got the same problem.

>Sys.setenv(RGSCMD="/TJPROJ1/RNA/WORK/software/Ghostscript/ghostscript-9.26-linux-x8664/gs") >pcms <- readPCM(file.path(find.package("motifStack"),"extdata"),"pcm$") >motifs <- lapply(pcms,pcm2pfm) >motifStack(motifs,layout="stack",ncex=1.0)

* caught segfault * address 0x7f3e00000000, cause 'memory not mapped'

Traceback: 1: xmlTreeParse(rgmlFile, ...) 2: readPicture(paste(psfilename, ".xml", sep = "")) 3: coloredSymbols(ncha, font, colset, rname, fontsize) 4: plotMotifLogo(pfm = x@mat, motifName = x@name, p = x@background[rownames(x@mat)], colset = x@color[rownames(x@mat)], ...) 5: plot(pfms[[n - i + 1]], xlab = NA, ...) 6: plot(pfms[[n - i + 1]], xlab = NA, ...) 7: plotMotifLogoStack(pfms, ...) 8: motifStack(motifs, layout = "stack", ncex = 1)

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

Here is the sessionInfo of motifStack, before the "motifStack" command. Hope it could be helpful.

>sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final)

Matrix products: default BLAS: /PUBLIC/software/RNA/R/R-3.5.1/lib64/R/lib/libRblas.so LAPACK: /PUBLIC/software/RNA/R/R-3.5.1/lib64/R/lib/libRlapack.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C
[3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LCPAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel grid stats graphics grDevices utils
[8] datasets methods base

other attached packages: [1] motifStack1.26.0 Biostrings2.50.2 XVector0.22.0
[4] IRanges2.16.0 S4Vectors0.20.1 ade41.7-13
[7] MotIV1.38.0 BiocGenerics0.28.0 grImport0.9-1.1
[10] XML3.98-1.16

loaded via a namespace (and not attached): [1] Rcpp1.0.0 MASS7.3-51.1
[3] GenomicRanges1.34.0 zlibbioc1.28.0
[5] GenomicAlignments1.18.1 munsell0.5.0
[7] BiocParallel1.16.5 colorspace1.4-0
[9] BSgenome1.50.0 lattice0.20-38
[11] GenomeInfoDb1.18.1 tools3.5.1
[13] SummarizedExperiment1.12.0 Biobase2.42.0
[15] seqLogo1.48.0 htmltools0.3.6
[17] matrixStats0.54.0 digest0.6.18
[19] Matrix1.2-15 GenomeInfoDbData1.2.0
[21] rtracklayer1.42.1 htmlwidgets1.3
[23] bitops1.0-6 RCurl1.95-4.11
[25] rGADEM2.30.0 DelayedArray0.8.0
[27] compiler3.5.1 scales1.0.0
[29] Rsamtools_1.34.0

Thanks,

Zixi

ADD REPLY • link 5.8 years ago chenzixi07 • 0

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Entering edit mode

BTW, ATACseqQC works well on my own Windows-based R-3.5.1, but "usually" failed on the footprint module on the CentOS server. Why I said "usually"? In fact I have successfully plot the footprint for the first time, but the segfault came back over and over again when I re-run the same script, and I still could not repeat the plot with the sample data.

Here is the sessionInfo after loading ATACseqQC, hope it could be helpful.

>sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final)

Matrix products: default BLAS: /PUBLIC/software/RNA/R/R-3.5.1/lib64/R/lib/libRblas.so LAPACK: /PUBLIC/software/RNA/R/R-3.5.1/lib64/R/lib/libRlapack.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C
[3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8
[5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LCPAPER=enUS.UTF-8 LCNAME=C
[9] LCADDRESS=C LCTELEPHONE=C
[11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] ATACseqQC1.6.4 S4Vectors0.20.1 BiocGenerics_0.28.0

loaded via a namespace (and not attached): [1] ProtGenerics1.14.0 bitops1.0-6
[3] matrixStats0.54.0 bit640.9-7
[5] progress1.2.0 httr1.4.0
[7] GenomeInfoDb1.18.1 tools3.5.1
[9] R62.3.0 rGADEM2.30.0
[11] KernSmooth2.23-15 seqLogo1.48.0
[13] DBI1.0.0 lazyeval0.2.1
[15] colorspace1.4-0 ade41.7-13
[17] motifStack1.26.0 prettyunits1.0.2
[19] bit1.1-14 curl3.3
[21] compiler3.5.1 VennDiagram1.6.20
[23] graph1.60.0 Biobase2.42.0
[25] formatR1.5 DelayedArray0.8.0
[27] grImport0.9-1.1 rtracklayer1.42.1
[29] scales1.0.0 randomForest4.6-14
[31] RBGL1.58.1 stringr1.3.1
[33] digest0.6.18 Rsamtools1.34.0
[35] XVector0.22.0 pkgconfig2.0.2
[37] htmltools0.3.6 ensembldb2.6.3
[39] limma3.38.3 BSgenome1.50.0
[41] regioneR1.14.0 htmlwidgets1.3
[43] rlang0.3.1 RSQLite2.1.1
[45] shiny1.2.0 BiocParallel1.16.5
[47] RCurl1.95-4.11 magrittr1.5
[49] polynom1.3-9 GO.db3.7.0
[51] GenomeInfoDbData1.2.0 futile.logger1.4.3
[53] Matrix1.2-15 Rcpp1.0.0
[55] munsell0.5.0 stringi1.2.4
[57] yaml2.2.0 MASS7.3-51.1
[59] SummarizedExperiment1.12.0 zlibbioc1.28.0
[61] AnnotationHub2.14.2 grid3.5.1
[63] blob1.1.1 promises1.0.1
[65] crayon1.3.4 lattice0.20-38
[67] Biostrings2.50.2 splines3.5.1
[69] multtest2.38.0 GenomicFeatures1.34.1
[71] hms0.4.2 GenomicScores1.6.0
[73] MotIV1.38.0 GenomicRanges1.34.0
[75] seqinr3.4-5 biomaRt2.38.0
[77] futile.options1.0.1 XML3.98-1.16
[79] lambda.r1.2.3 BiocManager1.30.4
[81] idr1.2 httpuv1.4.5.1
[83] assertthat0.2.0 mime0.6
[85] preseqR4.0.0 xtable1.8-3
[87] AnnotationFilter1.6.0 later0.7.5
[89] survival2.43-3 ChIPpeakAnno3.16.1
[91] GenomicAlignments1.18.1 AnnotationDbi1.44.0
[93] memoise1.1.0 IRanges2.16.0
[95] interactiveDisplayBase_1.20.0

ADD REPLY • link 5.8 years ago chenzixi07 • 0

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Hi Jianhong,

I want to mention that even without setting the R_GSCMD (which means R could not find ghostscript), running the sample script of ATACseqQC still get the 'memory not mapped' fault.

In addition, if using a plot saving command (like CairoPNG("FP.png")) before the factorFootprints command, I could get a footprint plot without the motif logo after R breakdown. It looks like someting goes wrong with motifStack, but I do not know what happend.

Besides, I tested ATACseqQC on my own WLS ubuntu and it works well. On my own WLS ubuntu, all the requied system libs were installed using apt-get install. However on the server, some libs were installed manually from source to my own HOME_PATH and exported in bash_profile. Is it possible that I forgot to export some libs?

Zixi

ADD REPLY • link 5.8 years ago chenzixi07 • 0

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Hi Zixi,

Sorry for the late reply. I tried to repeat your error in centOS 6.10 (docker to centOS 6.6 is not working). However I can not repeat it. I think main issue may be caused by the library of libxml2-devel or curl-devel. You can have a try to reinstall the grImport by giving it correct libxml2 lib and include path by Makevars file.

The testing docker:https://hub.docker.com/r/jianhong/motifstackcentos

ADD REPLY • link 5.8 years ago Ou, Jianhong ★ 1.3k

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Hi Jianhong, Thanks for your reply. I did not noticed the library of libxml2. After intalling libxml2 2.9.9, export the PATH, and reinstall the XML package in R, I could plot the footprint! Thanks!

Zixi

ADD REPLY • link 5.8 years ago chenzixi07 • 0

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Hi Zixi,

Great to know you figure it out!

Jianhong

ADD REPLY • link 5.8 years ago Ou, Jianhong ★ 1.3k