> Actually this is now a different problem in that your database is
> locked…You may want to try to move the cuffData.db file to a different
> location (keep it as a backup) and then try to rebuild.
>

Sorry, I wasn't precise enough I tried it before but no change.

I'll try with the new version, I hope I can still use the old transcript
assemblies from cufflinks-1.3 :)


Thanks for help!



> My guess is that you are using an older version.  I would highly recommend
> that you run the most recent version of cuffdiff if possible, for numerous
> reasons, least of which is compatibility with the new cummerbund.
>
> Cheers,
> Loyal
>
> On Oct 8, 2012, at 12:35 PM, Michael <mllmmllmmllmm@gmail.com> wrote:
>
> hard to check at the moment, I'll ask our admin; but unfortunately, it's
> rather an old version as this on galaxy
>
> i tried cuff<-readCufflinks(rebuild=T), the same problem
>
>
> Creating database
> /Users/mbi/Desktop/RNAseq/cummerbund/replicatesnew/cuffData.db
> Error in sqliteExecStatement(con, statement, bind.data) :
>   RS-DBI driver: (error in statement: database is locked)
>
>
>
> On Mon, Oct 8, 2012 at 6:17 PM, Loyal A. Goff <lgoff@csail.mit.edu> wrote:
>
>> The new version of cummerbund is designed to work with cuffdiff >=2.0.0,
>> and therefore if you have a cuffdiff analysis generated prior to cuffdiff
>> 2.0, there may be some functionality that is not available.
>>
>> Are you working on a dataset that you had previously used with an earlier
>> version of cummerbund?  There have been a few changes to the underlying DB
>> schema for one, and it is always a good idea when you update cummerbund to
>> rebuild the database backend on previous analyses:
>>
>> cuff<-readCufflinks(rebuild=T)
>>
>> This will adjust the schema accordingly, and if you do have the relevant
>> output from cuffdiff2, this will now be integrated into the cuffData.db
>> backend.
>>
>> The error that you are getting from dispersionPlot() suggests to me that
>> there may not be the pertinent information from cuffdiff2 available in your
>> output..
>>
>> What version of cuffdiff was used to generate your output?
>>
>> -Loyal
>>
>>
>> On Oct 8, 2012, at 11:53 AM, Micheal [guest] <guest@bioconductor.org>
>> wrote:
>>
>> >
>> > Hi,
>> >
>> > I have experianced mutliple errors when plotting using cummerbund 2.0
>> but only some functions, and it works on the demo dataset.
>> >
>> > My is data from replicates and density plots works - dens(), but not
>> the densrep() function, can this be a problem of the cuffdiff version?
>> >
>> > Here is also session info:
>> >
>> > R version 2.15.1 (2012-06-22)
>> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> >
>> > locale:
>> > [1] C/en_US.UTF-8/C/C/C/C
>> >
>> > attached base packages:
>> > [1] grid      stats     graphics  grDevices utils     datasets  methods
>>   base
>> >
>> > other attached packages:
>> > [1] BiocInstaller_1.8.1  cummeRbund_2.0.0     Gviz_1.2.0
>> rtracklayer_1.18.0   GenomicRanges_1.10.1
>> > [6] IRanges_1.16.2       fastcluster_1.1.7    reshape2_1.2.1
>> ggplot2_0.9.2.1      RSQLite_0.11.2
>> > [11] DBI_0.2-5            BiocGenerics_0.4.0
>> >
>> > loaded via a namespace (and not attached):
>> > [1] AnnotationDbi_1.20.0   BSgenome_1.26.0        Biobase_2.18.0
>>   Biostrings_2.26.1
>> > [5] GenomicFeatures_1.10.0 Hmisc_3.9-3            MASS_7.3-22
>>  RColorBrewer_1.0-5
>> > [9] RCurl_1.95-0.1.2       Rsamtools_1.10.1       XML_3.95-0.1
>>   biomaRt_2.14.0
>> > [13] biovizBase_1.6.0       bitops_1.0-4.1         cluster_1.14.2
>>   colorspace_1.1-1
>> > [17] dichromat_1.2-4        digest_0.5.2           gtable_0.1.1
>>   labeling_0.1
>> > [21] lattice_0.20-10        memoise_0.1            munsell_0.4
>>    parallel_2.15.1
>> > [25] plyr_1.7.1             proto_0.3-9.2          scales_0.2.2
>>   stats4_2.15.1
>> > [29] stringr_0.6.1          tools_2.15.1           zlibbioc_1.4.0
>> >
>> > -- output of sessionInfo():
>> >
>> >> disp<-dispersionPlot(genes(cuff))
>> >> disp
>> > Error in layout_base(data, vars, drop = drop) :
>> >  Faceting variables must have at least one value
>> >
>> >> genes.scv<-fpkmSCVPlot(genes(cuff))
>> > Error in sqliteExecStatement(con, statement, bind.data) :
>> >  RS-DBI driver: (error in statement: near ")": syntax error)
>> >> isoforms.scv<-fpkmSCVPlot(isoforms(cuff))
>> > Error in sqliteExecStatement(con, statement, bind.data) :
>> >  RS-DBI driver: (error in statement: near ")": syntax error)
>> >
>> >> densRep<-csDensity(genes(cuff),replicates=T)
>> > Error in sqliteExecStatement(con, statement, bind.data) :
>> >  RS-DBI driver: (error in statement: near ")": syntax err
>> >
>> > --
>> > Sent via the guest posting facility at bioconductor.org.
>>
>>
>
>

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