[Bioc-devel] rJava .jpackage("RDAVIDWebService") segfaults in restored R session

[Cook, Malcolm]

Hi,

I'm having trouble making a minimal reproducible example, but, pretty reliably I get the following segfault calling DAVIDWebService in a restored R session:

> david<-DAVIDWebService$new(email="mec at stowers.org")

  *** caught segfault ***
 address 0x7f5b1bd0e000, cause 'invalid permissions'

 Traceback:
  1: .External(interface, obj at jobj, returnSig, method, ...)
  2: .jcall(.rJava.class.loader, "V", "addClassPath", as.character(path))
  3: .jaddClassPath(jars)
  4: .jpackage("RDAVIDWebService")
  5: stopifnot(.jpackage("RDAVIDWebService"))
  6: .Object$initialize(...)
  7: initialize(value, ...)
  8: initialize(value, ...)
  9: methods::new(def, ...)
 10: DAVIDWebService$new(email = "mec at stowers.org")

I suspect something needs reinitialization re: the rJava JVM, perhaps due to some interaction with XLConnect, which also uses rJava. 

But, I am at a loss for how to sleuth this out.  Any hints or advice for sleuthing/fixing are VERY WELCOME.

And, thanks for rJava and DAVIDWebService,

Below is output of restoring the session, loading some libraries, and sessionInfo() immediately before the segfaulting call.

~ malcolm_cook at stowers.org




 R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
 Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)

 R is free software and comes with ABSOLUTELY NO WARRANTY.
 You are welcome to redistribute it under certain conditions.
 Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

 R is a collaborative project with many contributors.
 Type 'contributors()' for more information and
 'citation()' on how to cite R or R packages in publications.

 Type 'demo()' for some demos, 'help()' for on-line help, or
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.

 Loading required package: DBI
 Loading required package: AnnotationDbi
 Loading required package: BiocGenerics
 Loading required package: graphics
 Loading required package: stats
 Loading required package: parallel

 Attaching package: ‘BiocGenerics’

 The following objects are masked from ‘package:parallel’:

     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

 The following object is masked from ‘package:stats’:

     xtabs

 The following objects are masked from ‘package:base’:

     anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmi\
 n, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist

 Loading required package: Biobase
 Welcome to Bioconductor

     Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.


 [Previously saved workspace restored]

 During startup - Warning message:
 no function found corresponding to methods exports from ‘RDAVIDWebService’ for: ‘universeCounts’, ‘universeMappedCount’
 > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
 > library(RDAVIDWebService)

 source('../../../dap/R/util.R')

 Loading required package: rJava
 Loading required package: ggplot2
 Loading required package: GO.db
 Loading required package: graph
 Loading required package: Category
 Loading required package: Matrix
 Loading required package: GOstats

 Attaching package: ‘GOstats’

 The following object is masked from ‘package:AnnotationDbi’:

     makeGOGraph

 Loading required package: RBGL

 Attaching package: ‘RDAVIDWebService’

 The following object is masked from ‘package:AnnotationDbi’:

     species

 The following object is masked from ‘package:BiocGenerics’:

     counts

 >
 >

 Attaching package: ‘svUnit’

 The following object is masked from ‘package:AnnotationDbi’:

     metadata


 Attaching package: ‘compare’

 The following object is masked from ‘package:base’:

     isTRUE

 Loading required package: plyr

 Attaching package: ‘plyr’

 The following object is masked from ‘package:graph’:

     join


 Attaching package: ‘reshape’

 The following objects are masked from ‘package:plyr’:

     rename, round_any

 The following object is masked from ‘package:Matrix’:

    expand

 Registering fonts with R
 data.table 1.9.2  For help type: help("data.table")

 Attaching package: ‘IRanges’

 The following objects are masked from ‘package:reshape’:

     expand, rename

 The following objects are masked from ‘package:plyr’:

     desc, rename

 The following object is masked from ‘package:compare’:

     compare

 The following object is masked from ‘package:svUnit’:

     metadata

 The following object is masked from ‘package:RDAVIDWebService’:

     members

 The following object is masked from ‘package:Matrix’:

     expand

 Loading required package: XVector

 Attaching package: ‘XVector’

 The following object is masked from ‘package:plyr’:

     compact


 Attaching package: ‘GenomicRanges’

 The following object is masked from ‘package:data.table’:

     last


 Attaching package: ‘GenomicFeatures’

 The following object is masked from ‘package:RDAVIDWebService’:

     genes

 Loading required package: Biostrings

 Attaching package: ‘Biostrings’

 The following object is masked _by_ ‘.GlobalEnv’:
    tb

 The following object is masked from ‘package:RDAVIDWebService’:

     type

 The following object is masked from ‘package:graph’:

     complement


 Attaching package: ‘BSgenome’

 The following object is masked from ‘package:RDAVIDWebService’:

     species

 The following object is masked from ‘package:AnnotationDbi’:

     species

 Loading required package: R2HTML
 Loading required package: RColorBrewer

 Attaching package: ‘latticeExtra’

 The following object is masked from ‘package:ggplot2’:

     layer

 XLConnect 0.2-7 by Mirai Solutions GmbH
 http://www.mirai-solutions.com ,
 http://miraisolutions.wordpress.com



!> sessionInfo()
 R version 3.0.2 (2013-09-25)
 Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

 other attached packages:
  [1] edgeR_3.4.2            limma_3.18.13          XLConnect_0.2-7        latticeExtra_0.6-26    RColorBrewer_1.0-5     lattice_0.20-27        HTMLUtils_0.1.5        R2HTML_2.2.1           BSgenome_1.30.0 \
        rtracklayer_1.22.5     Rsamtools_1.14.3       Biostrings_2.30.1      GenomicFeatures_1.14.5 GenomicRanges_1.14.4   XVector_0.2.0          IRanges_1.20.7         data.table_1.9.2       Cairo_1.5-5   \
          extrafont_0.16         stringr_0.6.2          gtools_3.3.1           reshape_0.8.4          plyr_1.8.1             functional_0.4         compare_0.2-4
 [26] svUnit_0.7-12          RSvgDevice_0.6.4.3     RDAVIDWebService_1.0.0 RBGL_1.38.0            GOstats_2.28.0         Category_2.28.0        Matrix_1.1-2-2         graph_1.40.1           GO.db_2.10.1    \
        ggplot2_0.9.3.1        rJava_0.9-6            AnnotationDbi_1.24.0   Biobase_2.22.0         BiocGenerics_0.8.0     RSQLite_0.11.4         DBI_0.2-7

 loaded via a namespace (and not attached):
  [1] annotate_1.40.1       AnnotationForge_1.4.4 biomaRt_2.18.0        bitops_1.0-6          colorspace_1.2-4      compiler_3.0.2        dichromat_2.0-0       digest_0.6.4          extrafontdb_1.0       ge\
 nefilter_1.44.0     GSEABase_1.24.0       gtable_0.1.2          labeling_0.2          MASS_7.3-30           munsell_0.4.2         proto_0.3-10          Rcpp_0.11.0           RCurl_1.95-4.1        reshape2_\
 1.2.2        Rttf2pt1_1.3          scales_0.2.3          splines_3.0.2         stats4_3.0.2          survival_2.37-7       tools_3.0.2           VennDiagram_1.6.5     XML_3.98-1.1
 [28] xtable_1.7-3          zlibbioc_1.8.0