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Halian Vilela
▴
50
@halian-vilela-4954
Last seen 10.3 years ago
Hi guys, this week I've managed to construct a TranscripDb object from
the
gene database I was using for analysis, and for my surprise every time
I
try to use the saved txdb data my Rsession crashes!
When I generate a fresh object using the makeTranscriptDb() function
everything works flawlessly, but whenever I save the object (with
save() or
when the object is within a saved workspace) and try to reload it then
R
crashes. I'm using the Rstudio IDE, so it realy crashes and exit the
program. If I try to use it in the command line interface, then I get
the
following traceback:
##################################### TRACEBACK
#########################################
> txdb
TranscriptDb object:
Traceback:
1: .Call("RS_SQLite_exec", conId, statement, bind.data, PACKAGE =
.SQLitePkgName)
2: sqliteExecStatement(con, statement, bind.data)
3: sqliteQuickSQL(conn, statement, ...)
4: dbGetQuery(con, paste("SELECT * from", name))
5: dbGetQuery(con, paste("SELECT * from", name))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch(expr, error = function(e) { call <- conditionCall(e)
if
(!is.null(call)) { if (identical(call[[1L]],
quote(doTryCatch)))
call <- sys.call(-4L) dcall <- deparse(call)[1L]
prefix <- paste("Error in",
dcall, ": ") LONG <- 75L msg <- conditionMessage(e)
sm
<- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type =
"w") +
nchar(sm[1L], type = "w") if is.na(w)) w <- 14L +
nchar(dcall, type = "b") + nch
ar(sm[1L], type = "b") if (w > LONG)
prefix <- paste(prefix, "\n ", sep = "") } else prefix <-
"Error : "
msg <- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1L])) i
f (!silent && identical(getOption("show.error.messages"),
TRUE)) {
cat(msg, file = stderr())
.Internal(printDeferredWarnings())
} invisible(structure(msg, class = "try-error", condition =
e))})
10: try(dbGetQuery(con, paste("SELECT * from", name)))
11: sqliteReadTable(conn, name, ...)
12: is(object, Cl)
13: is(object, Cl)
14: .valueClassTest(standardGeneric("dbReadTable"), "data.frame",
"dbReadTable")
15: dbReadTable(dbConn(x), "metadata")
16: .local(x, ...)
17: metadata(object)
18: metadata(object)
19: function (object) standardGeneric("show")(<s4 object="" of="" class="" "transcriptdb"="">)
20: function (object) standardGeneric("show")(<s4 object="" of="" class="" "transcriptdb"="">)
Error in sqliteExecStatement(con, statement, bind.data) :
caught access violation - continue with care
Error in sqliteReadTable(conn, name, ...) : could not find table
metadata
######################################## TRACEBACK END
############################################
So what's may be going on ? I've already checked my versions, all
Bioconductor packages are up to date, and as I said, it works without
any
errors if I just recreate the object. But this approach is very
clumbersome
because I'm using multiple machines so I have to share data constantly
between them, the ideal approach would be being able to save the
object and
use it.
Oh, it alse works if I use saveFeatures() to dump and then use
loadFeatures() to recover, but I still thinks it's not as practical
because
I'll never get a totally functional workspace I one of the objects
crashes
my session and I have to reload it every time I want to use it.
Thanks a lot,
Halian
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252
[3] LC_MONETARY=Portuguese_Brazil.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Brazil.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures_1.6.4 AnnotationDbi_1.16.5 Biobase_2.14.0
[4] GenomicRanges_1.6.4 IRanges_1.12.3
loaded via a namespace (and not attached):
[1] biomaRt_2.10.0 Biostrings_2.22.0 BSgenome_1.22.0
DBI_0.2-5
[5] RCurl_1.7-0.1 RSQLite_0.10.0 rtracklayer_1.14.4
tools_2.14.0
[9] XML_3.4-2.2 zlibbioc_1.0.0
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