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

[Martin Morgan]

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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