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

Shepherd, Lori Lori.Shepherd at RoswellPark.org
Tue Apr 17 15:38:40 CEST 2018


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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