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 [[alternative HTML version deleted]]

On 12/03/2011 07:44 AM, Halian Vilela wrote: > 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 Hi Halian -- As you've discovered the right thing to do is to use saveFeatures / loadFeatures. The problem is that the object contains a connection to the SQLite data base, and that connection is not being saved and restored correctly. In some ways it can't always be saved and restored, e.g., if between R sessions you were to change the location where the data base were stored. So I think the base expectation is 'it won't work to save() / load()'. At the same time it shouldn't crash your R session. I think the problem is lower in the hierarchy, e.g., library(RSQLite) m <- dbDriver("SQLite") con <- dbConnect(m, dbname = tempfile()) data(USArrests) dbWriteTable(con, "USArrests", USArrests) ## read on an expired connection segfaults dbDisconnect(con) dbReadTable(con, "USArrests") I'll bring this to the attention of the RSQLite maintainer. Thanks for the report. Martin > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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