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$new(email="m...@stowers.org")
*** caught segfault ***
address 0x7f5b1bd0e000, cause 'invalid permissions'
Traceback:
1: .External(interface, obj@jobj, returnSig, method, ...)
2: .jcall(.rJava.class.loader, "V", "addClassPath", as.character(path))
3: .jaddClassPath(jars)
4: .jpackage("RDAVIDWebService")
5: stopifnot(.jpackage("RDAVIDWebService"))
6: .Object$initialize(...)
7: initialize(value, ...)
8: initialize(value, ...)
9: methods::new(def, ...)
10: DAVIDWebService$new(email = "m...@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_c...@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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
