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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