[Rcpp-devel] I'm having trouble installing packages that seem to be related to segfault with Rcpp

Keith O'Hara kth.ohr at gmail.com
Tue Apr 17 17:35:32 CEST 2018


Just a suggestion, but I was running into package-related segfaults on Rdevel last week. I believe Martin Maechler committed a fix for some of these issues on Sunday. Might be worth checking if these errors are visible using the latest Rdevel or just the RC.

Keith

> On Apr 17, 2018, at 11:04 AM, Martin Morgan <martin.morgan at roswellpark.org> wrote:
> 
> The stack trace looks like it's an Rcpp problem (topic of this mailing list) maybe with a finalizer running at an unexpected time for what it wants to accomplish. R-3.5 is in release candidate so highly relevant to the user community even if not R-devel. If this list can help rule out Rcpp or help point to the offending user of Rcpp or otherwise identify the problem that would be great...
> 
> Martin
> 
>>> On 04/17/2018 10:55 AM, Jeff Newmiller wrote:
>>> R v3.5 is still off-topic on this mailing list. Try R-devel.
>>> On April 17, 2018 6:38:40 AM PDT, "Shepherd, Lori" <Lori.Shepherd at RoswellPark.org> wrote:
>>> I starting running into an issue trying to install certain packages
>>> where I encounter a segfault.  I can also install packages but then
>>> upon quitting R I get a segfault.
>>> 
>>> 
>>> lori at lori-HP-ZBook-15-G2:~$ R CMD config CC
>>> gcc
>>> lori at lori-HP-ZBook-15-G2:~$ R CMD config CXX
>>> g++
>>> 
>>> lori at lori-HP-ZBook-15-G2:~$ g++ --version
>>> g++ (Ubuntu 5.4.1-2ubuntu1~14.04) 5.4.1 20160904
>>> Copyright (C) 2015 Free Software Foundation, Inc.
>>> This is free software; see the source for copying conditions.  There is
>>> NO
>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>>> PURPOSE.
>>> 
>>> lori at lori-HP-ZBook-15-G2:~$ gcc --version
>>> gcc (Ubuntu 5.4.1-2ubuntu1~14.04) 5.4.1 20160904
>>> Copyright (C) 2015 Free Software Foundation, Inc.
>>> This is free software; see the source for copying conditions.  There is
>>> NO
>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>>> PURPOSE.
>>> 
>>> 
>>> 
>>> 
>>> As an example.  I was trying to install the package erma.
>>> http://bioconductor.org/packages/release/bioc/html/erma.html
>>> 
>>> According to the description it seems like shiny and ggplot2 are likely
>>> the only dependencies that would load Rcpp
>>> 
>>> 
>>> lori at lori-HP-ZBook-15-G2:~/b/Rpacks$ R CMD INSTALL --no-test-load erma
>>> Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help
>>> * installing to library
>>> '/home/lori/R/x86_64-pc-linux-gnu-library/3.5-BioC-3.7'
>>> * installing *source* package 'erma' ...
>>> ** R
>>> ** data
>>> ** inst
>>> ** byte-compile and prepare package for lazy loading
>>> ** help
>>> *** installing help indices
>>> ** building package indices
>>> ** installing vignettes
>>> * DONE (erma)
>>> 
>>> *** caught segfault ***
>>> address (nil), cause 'memory not mapped'
>>> An irrecoverable exception occurred. R is aborting now ...
>>> Segmentation fault
>>> 
>>> 
>>> 
>>> The package installed but then when I do a library("erma") and quit R
>>> the segfault message also appears. When I tried debugging with
>>> valgrind, it provided the following output:
>>> 
>>> 
>>> 
>>> lori at lori-HP-ZBook-15-G2:/tmp/Rcpp$ cat erma.valgrind
>>> ==22933== Memcheck, a memory error detector
>>> ==22933== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et
>>> al.
>>> ==22933== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright
>>> info
>>> ==22933== Command: /home/lori/bin/R-3-5-branch/bin/exec/R -e
>>> library(erma)
>>> ==22933==
>>> 
>>> R version 3.5.0 beta (2018-04-09 r74559) -- "Joy in Playing"
>>> Copyright (C) 2018 The R Foundation for Statistical Computing
>>> Platform: x86_64-pc-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.
>>> 
>>> Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help
>>>> library(erma)
>>> Loading required package: Homo.sapiens
>>> Loading required package: AnnotationDbi
>>> Loading required package: stats4
>>> Loading required package: BiocGenerics
>>> 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 objects are masked from 'package:stats':
>>> 
>>>    IQR, mad, sd, var, xtabs
>>> 
>>> The following objects are masked from 'package:base':
>>> 
>>>    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
>>>    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
>>>    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
>>>    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
>>>    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
>>>    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
>>>    unsplit, which, which.max, which.min
>>> 
>>> 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")'.
>>> 
>>> Loading required package: IRanges
>>> Loading required package: S4Vectors
>>> 
>>> Attaching package: 'S4Vectors'
>>> 
>>> The following object is masked from 'package:base':
>>> 
>>>    expand.grid
>>> 
>>> Loading required package: OrganismDbi
>>> Loading required package: GenomicFeatures
>>> Loading required package: GenomeInfoDb
>>> Loading required package: GenomicRanges
>>> Loading required package: GO.db
>>> 
>>> Loading required package: org.Hs.eg.db
>>> 
>>> Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
>>> Loading required package: GenomicFiles
>>> Loading required package: SummarizedExperiment
>>> Loading required package: DelayedArray
>>> Loading required package: matrixStats
>>> 
>>> Attaching package: 'matrixStats'
>>> 
>>> The following objects are masked from 'package:Biobase':
>>> 
>>>    anyMissing, rowMedians
>>> 
>>> Loading required package: BiocParallel
>>> 
>>> Attaching package: 'DelayedArray'
>>> 
>>> The following objects are masked from 'package:matrixStats':
>>> 
>>>    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
>>> 
>>> The following objects are masked from 'package:base':
>>> 
>>>    aperm, apply
>>> 
>>> Loading required package: Rsamtools
>>> Loading required package: Biostrings
>>> Loading required package: XVector
>>> 
>>> Attaching package: 'Biostrings'
>>> 
>>> The following object is masked from 'package:DelayedArray':
>>> 
>>>    type
>>> 
>>> The following object is masked from 'package:base':
>>> 
>>>    strsplit
>>> 
>>> Loading required package: rtracklayer
>>> ==22933== Invalid read of size 4
>>> ==22933==    at 0x8CC0443: std::locale::~locale() (in
>>> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19)
>>> ==22933==    by 0x1DDE0572: ~basic_streambuf (streambuf:198)
>>> ==22933==    by 0x1DDE0572: ~Rstreambuf (Rstreambuf.h:31)
>>> ==22933==    by 0x1DDE0572: Rcpp::Rostream<false>::~Rostream()
>>> (Rstreambuf.h:44)
>>> ==22933==    by 0x6E2E1A8: __run_exit_handlers (exit.c:82)
>>> ==22933==    by 0x6E2E1F4: exit (exit.c:104)
>>> ==22933==    by 0x5EA95F: Rstd_CleanUp (sys-std.c:1213)
>>> ==22933==    by 0x511082: end_Rmainloop (main.c:1072)
>>> ==22933==    by 0x511082: run_Rmainloop (main.c:1083)
>>> ==22933==    by 0x41B607: main (Rmain.c:29)
>>> ==22933==  Address 0x0 is not stack'd, malloc'd or (recently) free'd
>>> ==22933==
>>> 
>>> *** caught segfault ***
>>> address (nil), cause 'memory not mapped'
>>> An irrecoverable exception occurred. R is aborting now ...
>>> ==22933==
>>> ==22933== HEAP SUMMARY:
>>> ==22933==     in use at exit: 577,597,056 bytes in 135,393 blocks
>>> ==22933==   total heap usage: 661,662 allocs, 526,269 frees,
>>> 1,380,607,407 bytes allocated
>>> ==22933==
>>> ==22933== LEAK SUMMARY:
>>> ==22933==    definitely lost: 0 bytes in 0 blocks
>>> ==22933==    indirectly lost: 0 bytes in 0 blocks
>>> ==22933==      possibly lost: 1,591,450 bytes in 2,158 blocks
>>> ==22933==    still reachable: 576,005,606 bytes in 133,235 blocks
>>> ==22933==         suppressed: 0 bytes in 0 blocks
>>> ==22933== Rerun with --leak-check=full to see details of leaked memory
>>> ==22933==
>>> ==22933== For counts of detected and suppressed errors, rerun with: -v
>>> ==22933== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from
>>> 0)
>>> 
>>> 
>>> 
>>> 
>>> Any advice on how to remedy this situation is greatly appreciated.
>>> 
>>> 
>>> 
>>> Lori Shepherd
>>> 
>>> Bioconductor Core Team
>>> 
>>> Roswell Park Cancer Institute
>>> 
>>> Department of Biostatistics & Bioinformatics
>>> 
>>> Elm & Carlton Streets
>>> 
>>> Buffalo, New York 14263
>>> 
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