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.sheph...@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@lori-HP-ZBook-15-G2:~$ R CMD config CC >gcc >lori@lori-HP-ZBook-15-G2:~$ R CMD config CXX >g++ > >lori@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@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@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@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 > > >This email message may contain legally privileged and/or confidential >information. 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