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

Jeff Newmiller jdnewmil at dcn.davis.ca.us
Tue Apr 17 16:55:20 CEST 2018


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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-- 
Sent from my phone. Please excuse my brevity.


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