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vjcitn/sessioinfo.txt

Created October 11, 2024 11:40
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ubuntu 24.04 gdb trace
Raw
sessioinfo.txt
> sessionInfo()
R version 4.4.1 Patched (2024-09-30 r87215)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] rtracklayer_1.64.0 GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
[4] IRanges_2.38.1 S4Vectors_0.42.1 BiocGenerics_0.50.0
[7] BiocFileCache_2.13.1 dbplyr_2.5.0
loaded via a namespace (and not attached):
[1] utf8_1.2.4 generics_0.1.3
[3] SparseArray_1.4.8 bitops_1.0-9
[5] lattice_0.22-6 RSQLite_2.3.7
[7] magrittr_2.0.3 grid_4.4.1
[9] fastmap_1.2.0 blob_1.2.4
[11] Matrix_1.7-0 jsonlite_1.8.9
[13] restfulr_0.0.15 DBI_1.2.3
[15] httr_1.4.7 purrr_1.0.2
[17] fansi_1.0.6 UCSC.utils_1.0.0
[19] XML_3.99-0.17 Biostrings_2.72.1
[21] codetools_0.2-20 abind_1.4-8
[23] cli_3.6.3 rlang_1.1.4
[25] crayon_1.5.3 XVector_0.44.0
[27] Biobase_2.64.0 bit64_4.5.2
[29] DelayedArray_0.30.1 withr_3.0.1
[31] cachem_1.1.0 yaml_2.3.10
[33] S4Arrays_1.4.1 parallel_4.4.1
[35] tools_4.4.1 BiocParallel_1.38.0
[37] memoise_2.0.1 dplyr_1.1.4
[39] Rsamtools_2.20.0 GenomeInfoDbData_1.2.12
[41] filelock_1.0.3 SummarizedExperiment_1.34.0
[43] curl_5.2.3001 vctrs_0.6.5
[45] R6_2.5.1 matrixStats_1.4.1
[47] BiocIO_1.14.0 lifecycle_1.0.4
[49] zlibbioc_1.50.0 bit_4.5.0
[51] pkgconfig_2.0.3 pillar_1.9.0
[53] glue_1.8.0 GenomicAlignments_1.40.0
[55] tibble_3.2.1 tidyselect_1.2.1
[57] MatrixGenerics_1.16.0 rjson_0.2.23
[59] compiler_4.4.1 RCurl_1.98-1.16
>
Raw
simp.R
library(BiocFileCache)
bfc = BiocFileCache()
url <- "http://httpbin.org/get"
add5 <- bfcadd(bfc, "TestWeb", fpath=url)
url2<- "https://en.wikipedia.org/wiki/Bioconductor"
#url2 <- "http://example.com"
add6 <- bfcadd(bfc, "TestWeb", fpath=url2)
rid6 <- names(add6)
# add a remote resource but don't initially download
add7 <- bfcadd(bfc, "TestNoDweb", fpath=url2, download=FALSE)
rid7 <- names(add7)
# let's look at our BiocFileCache object now
bfc
bfcinfo(bfc)
path <- tempfile()
bfc <- BiocFileCache(path, ask = FALSE)
url <- paste(
"ftp://ftp.ensembl.org/pub/release-71/gtf",
"homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz",
sep="/")
# and if not start tracking it is using `bfcrpath`
suppressPackageStartupMessages({
library(rtracklayer)
})
# load the cache
path <- file.path(tempdir(), "tempCacheDir")
bfc <- BiocFileCache(path, ask=FALSE)
# the web resources of interest
url <- "ftp://ftp.ensembl.org/pub/release-71/gtf/homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz"
url2 <- "ftp://ftp.ensembl.org/pub/release-71/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_5.0.71.gtf.gz"
# if not in cache will download and create new entry
pathsToLoad <- bfcrpath(bfc, c(url, url2))
Raw
trace.txt
> bfc <- BiocFileCache(path, ask=FALSE)
> # the web resources of interest
> url <- "ftp://ftp.ensembl.org/pub/release-71/gtf/homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz"
> url2 <- "ftp://ftp.ensembl.org/pub/release-71/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_5.0.71.gtf.gz"
> # if not in cache will download and create new entry
> pathsToLoad <- bfcrpath(bfc, c(url, url2))
adding rname 'ftp://ftp.ensembl.org/pub/release-71/gtf/homo_sapiens/Homo_sapiens.GRCh37.71.gtf.gz'
Thread 1 "R" received signal SIGSEGV, Segmentation fault.
chunk_list_free (anchor=0x555555572938) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/bufq.c:152
warning: 152/build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/bufq.c: No such file or directory
#0 chunk_list_free (anchor=0x555555572938) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/bufq.c:152
#1 Curl_bufq_free (q=0x555555572938) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/bufq.c:244
#2 0x00007ffff41374d9 in http2_data_done.isra.0 (cf=0x55555b035060, data=0x555580af4600, premature=<optimized out>)
at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/http2.c:326
#3 0x00007ffff40dfb63 in cf_h2_cntrl (cf=0x55555b035060, data=0x555580af4600, event=<optimized out>, arg1=<optimized out>,
arg2=<optimized out>) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/http2.c:2489
#4 0x00007ffff412d80e in Curl_conn_cf_cntrl (arg2=0x0, arg1=0, event=2, ignore_result=<optimized out>, data=0x555580af4600,
cf=0x55555b035060) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/cfilters.c:501
#5 cf_cntrl_all.constprop.0 (conn=conn@entry=0x55555ba82a90, data=data@entry=0x555580af4600, ignore_result=ignore_result@entry=true,
event=event@entry=2, arg1=arg1@entry=0, arg2=0x0) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/cfilters.c:551
#6 0x00007ffff411b3d4 in Curl_conn_ev_data_detach (data=0x555580af4600, conn=0x55555ba82a90)
at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/cfilters.c:568
#7 Curl_detach_connection (data=<optimized out>) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/multi.c:972
#8 extract_if_dead (conn=conn@entry=0x55555ba82a90, data=0x555580af4600) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/url.c:819
#9 0x00007ffff411b51c in call_extract_if_dead (data=<optimized out>, conn=0x55555ba82a90, param=0x7ffffffef450)
at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/url.c:845
#10 0x00007ffff40bcd4d in Curl_conncache_foreach (data=0x555580af4600, connc=<optimized out>, param=0x7ffffffef450,
func=0x7ffff411b500 <call_extract_if_dead>) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/conncache.c:332
#11 0x00007ffff40febd9 in prune_dead_connections (data=0x555580af4600) at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/url.c:874
#12 create_conn (async=0x7ffffffef42f, in_connect=<synthetic pointer>, data=<optimized out>)
at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/url.c:3623
#13 Curl_connect (protocol_done=0x7ffffffef430, asyncp=0x7ffffffef42f, data=<optimized out>)
at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/url.c:3889
#14 multi_runsingle (multi=multi@entry=0x555557a54b10, nowp=nowp@entry=0x7ffffffef4f0, data=data@entry=0x555580af4600)
at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/multi.c:1924
#15 0x00007ffff40ff0d5 in curl_multi_perform (multi=0x555557a54b10, running_handles=running_handles@entry=0x7ffffffef5f0)
at /build/curl-ZfTNv6/curl-8.5.0/debian/build/lib/multi.c:2702
#16 0x00007ffff4af569b in curl_perform_with_interrupt (handle=0x555580af4600) at interrupt.c:47
#17 0x00007ffff4af3515 in R_curl_fetch_disk (url=<optimized out>, ptr=0x555580c850f8, path=0x555580cd54f8, mode=0x55555bcac310,
nonblocking=0x555555574810) at fetch.c:79
#18 0x00007ffff7b051de in R_doDotCall (fun=fun@entry=0x7ffff4af3390 <R_curl_fetch_disk>, nargs=nargs@entry=5,
cargs=cargs@entry=0x7fffffff01a0, call=call@entry=0x55555a091918) at dotcode.c:766
#19 0x00007ffff7b488a0 in bcEval_loop (ploc=ploc@entry=0x7fffffff0460) at eval.c:8691
#20 0x00007ffff7b5c3aa in bcEval (rho=0x555580cd96c8, body=0x55555a08d598) at eval.c:7524
#21 bcEval (body=0x55555a08d598, rho=0x555580cd96c8) at eval.c:7509
#22 0x00007ffff7b5c71b in Rf_eval (e=e@entry=0x55555a08d598, rho=rho@entry=0x555580cd96c8) at eval.c:1167
#23 0x00007ffff7b5e93f in R_execClosure (call=call@entry=0x555580cd97a8, newrho=newrho@entry=0x555580cd96c8, sysparent=<optimized out>,
rho=rho@entry=0x555580cd9c40, arglist=arglist@entry=0x555580cd9e00, op=op@entry=0x55555a08daa0) at eval.c:2398
#24 0x00007ffff7b5f787 in applyClosure_core (call=0x555580cd97a8, op=0x55555a08daa0, arglist=0x555580cd9e00, rho=0x555580cd9c40,
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