ensembldb
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jorainer
using EnsDb on sqlite file crash further RMariaDB connections
If I execute this code:
library(ensembldb)
dbfile <- system.file("extdata/EnsDb.Hsapiens.v86.sqlite", package = "EnsDb.Hsapiens.v86")
edb <- EnsDb(dbfile)
library(RMariaDB)
DBI::dbConnect(MariaDB(), default.file = "./.my.cnf", groups = "default")
It makes R crash:
Thread 1 "R" received signal SIGSEGV, Segmentation fault.
0x00007efe9956cb40 in pthread_mutex_lock () from /lib/x86_64-linux-gnu/libpthread.so.0
Here's the gdb backtrace:
Thread 1 "R" received signal SIGSEGV, Segmentation fault.
0x00007efe9956cb40 in pthread_mutex_lock () from /lib/x86_64-linux-gnu/libpthread.so.0
(gdb) bt
#0 0x00007efe9956cb40 in pthread_mutex_lock () from /lib/x86_64-linux-gnu/libpthread.so.0
#1 0x00007efe830517d3 in sqlite3_finalize (pStmt=0x55dbd1cd4740) at vendor/sqlite3/sqlite3.c:81567
#2 0x00007efe82fdee20 in SqliteResultImpl::~SqliteResultImpl (this=0x55dbd99ce850, __in_chrg=<optimized out>) at SqliteResultImpl.cpp:42
#3 0x00007efe82fd2ec3 in boost::checked_delete<SqliteResultImpl> (x=0x55dbd99ce850) at /usr/local/lib/R/site-library/BH/include/boost/core/checked_delete.hpp:34
#4 boost::scoped_ptr<SqliteResultImpl>::~scoped_ptr (this=0x55dbd1cd4750, __in_chrg=<optimized out>) at /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/scoped_ptr.hpp:88
#5 DbResult::~DbResult (this=0x55dbd1cd4740, __in_chrg=<optimized out>) at DbResult.cpp:20
#6 0x00007efe82fe7348 in Rcpp::standard_delete_finalizer<DbResult> (obj=0x55dbd1cd4740) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/XPtr.h:31
#7 Rcpp::finalizer_wrapper<DbResult, &Rcpp::standard_delete_finalizer<DbResult> > (p=<optimized out>) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/XPtr.h:39
#8 0x00007efe82fe7199 in Rcpp::XPtr<DbResult, Rcpp::PreserveStorage, &Rcpp::standard_delete_finalizer<DbResult>, false>::release (this=0x7fff5ed09738) at /usr/local/lib/R/site-library/Rcpp/include/Rcpp/XPtr.h:173
#9 result_release (res=...) at result.cpp:17
#10 0x00007efe7cbbc845 in _RMariaDB_result_release (resSEXP=0x55dbda853b08) at RcppExports.cpp:175
#11 0x00007efe99add652 in ?? () from /usr/local/lib/R/lib/libR.so
#12 0x00007efe99ae7d60 in Rf_eval () from /usr/local/lib/R/lib/libR.so
Tell me if you can't reproduce it, I could try to build an ad-hoc docker.
session info:
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 3.6.1 (2019-07-05)
os Debian GNU/Linux 9 (stretch)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2020-07-24
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
AnnotationDbi * 1.48.0 2019-10-29 [1] Bioconductor
AnnotationFilter * 1.10.0 2019-10-29 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 3.6.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
Biobase * 2.46.0 2019-10-29 [1] Bioconductor
BiocFileCache 1.10.2 2019-11-08 [1] Bioconductor
BiocGenerics * 0.32.0 2019-10-29 [1] Bioconductor
BiocParallel 1.20.1 2019-12-21 [1] Bioconductor
biomaRt 2.42.1 2020-03-26 [1] Bioconductor
Biostrings 2.54.0 2019-10-29 [1] Bioconductor
bit 1.1-14 2018-05-29 [1] CRAN (R 3.6.1)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.1)
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.1)
blob 1.2.0 2019-07-09 [1] CRAN (R 3.6.1)
callr 3.3.2 2019-09-22 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
curl 4.2 2019-09-24 [1] CRAN (R 3.6.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.1)
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 3.6.1)
DelayedArray 0.12.2 2020-01-06 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools 2.2.1 2019-09-24 [1] CRAN (R 3.6.1)
digest 0.6.22 2019-10-21 [1] CRAN (R 3.6.1)
dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1)
ensembldb * 2.10.2 2019-11-20 [1] Bioconductor
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
GenomeInfoDb * 1.22.0 2019-10-29 [1] Bioconductor
GenomeInfoDbData 1.2.2 2020-03-26 [1] Bioconductor
GenomicAlignments 1.22.1 2019-11-12 [1] Bioconductor
GenomicFeatures * 1.38.2 2020-02-15 [1] Bioconductor
GenomicRanges * 1.38.0 2019-10-29 [1] Bioconductor
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
hms 0.5.2 2019-10-30 [1] CRAN (R 3.6.1)
httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.1)
IRanges * 2.20.2 2020-01-13 [1] Bioconductor
lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
Matrix 1.2-17 2019-03-22 [2] CRAN (R 3.6.1)
matrixStats 0.55.0 2019-09-07 [1] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
openssl 1.4.1 2019-07-18 [1] CRAN (R 3.6.1)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1)
processx 3.4.2 2020-06-05 [1] Github (r-lib/processx@bfa8127)
progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.1)
ProtGenerics 1.18.0 2019-10-29 [1] Bioconductor
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.1)
purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.1)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.1)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.1)
Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
RCurl 1.95-4.12 2019-03-04 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
rlang 0.4.1 2019-10-24 [1] CRAN (R 3.6.1)
RMariaDB * 1.0.6 2018-05-06 [1] CRAN (R 3.6.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
Rsamtools 2.2.3 2020-02-23 [1] Bioconductor
RSQLite 2.1.2 2019-07-24 [1] CRAN (R 3.6.1)
rtracklayer 1.46.0 2019-10-29 [1] Bioconductor
S4Vectors * 0.24.4 2020-04-09 [1] Bioconductor
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.1)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
SummarizedExperiment 1.16.1 2019-12-19 [1] Bioconductor
testthat 2.3.0 2019-11-05 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.1)
usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)
XML 3.98-1.20 2019-06-06 [1] CRAN (R 3.6.1)
XVector 0.26.0 2019-10-29 [1] Bioconductor
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
zlibbioc 1.32.0 2019-10-29 [1] Bioconductor
Me neither with R in a docker container - maybe a forced reinstall of the RMariaDB package helps?
ok. Thanks for trying. I'll try to replicate it on another docker container (because it happened in a docker, but very very huge).