[BioC] makePdInfoPackage Error in sqliteExecStatement(con, statement, bind.data) : , bind.data must have non-zero dimensions

[Benilton Carvalho]

So we keep a record on the mailing list: the problem was due to the
fact that currently pdInfoBuilder expects to find the word
"experimental" in the PROBE_CLASS field for the experimental probes.
So, replacing "experiment" by "experimental" addressed the issue.

benilton

On 22 February 2012 06:11, mabawsa <mabawsa at gmail.com> wrote:
> Hi,
> I get "Error in sqliteExecStatement(con, statement, bind.data) : ,
>  bind.data must have non-zero dimensions" when run.
> It seems similar this error
> https://stat.ethz.ch/pipermail/bioconductor/2011-February/037796.html. I
> generated the pos file myself.
> I guess the SEQ_ID on the NDF file is strange but the entry at 194289 and
> 194290 seems to be OK.
>                    SEQ_ID MISMATCH PROBE_CLASS          PROBE_ID
> 194288    CHR9:46353-46389        0  experiment CHR0999P000090528
> 194289 CHR13:230623-230659        0  experiment CHR1300P000332204
> 194290 CHR13:595769-595805        0  experiment CHR1300P000337972
> 194291    CHR1:85497-85533        0  experiment CHR0100P000197636
>
> Any Help would be greatly appreciated...
>
>
> Here is my script
>
> library('oligo', quietly=TRUE)
> library('ff', quietly=TRUE)
> library('pdInfoBuilder', quietly=TRUE)
> library('genefilter', quietly=TRUE)
> library('limma', quietly=TRUE)
> library('RColorBrewer', quietly=TRUE)
> palette(brewer.pal(8, "Dark2"))
>
> data.dir <- "/microarray-data/ExtractedData/xys" #point to where the data is
> stored
> annotation.dir <- "/RNA/NASA/"
> xys.files <- list.xysfiles(data.dir, full.names = TRUE)
> pos.file <- list.files(annotation.dir, pattern=".pos", full.names = TRUE)
> ndf.file <- list.files(annotation.dir, pattern=".ndf", full.names = TRUE)
>
> ####################################################
> ## Make info package  MUST have only one POS and  ##
> ## NDF file in the directory                      ##
> ####################################################
> seed <- new("NgsTilingPDInfoPkgSeed",
>            ndfFile = ndf.file,
>            xysFile = xys.files[1],
>            posFile = pos.file,
>            author = "x",
>            email = "x at gmail.com",
>            biocViews = "AnnotationData",
>            genomebuild = "S288C_reference_genome_R49-1-1_20051216",
>            organism = "Yeast",
>            manufacturer="Nimblegen",
>            species = "Saccharomyces cerevisiae", url = "http://google.com")
>
> makePdInfoPackage(seed, destDir=annotation.dir)
>
>
> Here is my output:
>
> ================================================================================
> Building annotation package for Nimblegen Tiling Array
> NDF: 100507_NYW_BC396_NASA_Yeast_WG.ndf
> POS: 100507_NYW_BC396_NASA_Yeast_WG.pos
> XYS: 09_20_Expression_405004_S04.xys
> ================================================================================
> Parsing file: 100507_NYW_BC396_NASA_Yeast_WG.ndf... OK
> Parsing file: 100507_NYW_BC396_NASA_Yeast_WG.pos... OK
> Merging NDF and POS files... OK
> Parsing file: 09_20_Expression_405004_S04.xys... OK
> Creating package in
> /home/dougie/Documents/projects/RNA/NASA//pd.100507.nyw.bc396.nasa.yeast.wg
> Inserting 194289 rows into table featureSet... OK
> Inserting 0 rows into table pmfeature... Error in sqliteExecStatement(con,
> statement, bind.data) :
>  bind.data must have non-zero dimensions
>
>> traceback()
> 8: stop("bind.data must have non-zero dimensions")
> 7: sqliteExecStatement(con, statement, bind.data)
> 6: sqliteQuickSQL(conn, statement, bind.data, ...)
> 5: dbGetPreparedQuery(conn, sql_template, bind.data = data)
> 4: dbGetPreparedQuery(conn, sql_template, bind.data = data)
> 3: dbInsertDataFrame(conn, "pmfeature", parsedData[["pmFeatures"]],
>       tiledRegionPmFeatureSchema[["col2type"]], !quiet)
> 2: makePdInfoPackage(seed, destDir = annotation.dir)
> 1: makePdInfoPackage(seed, destDir = annotation.dir)
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] genefilter_1.36.0    Ringo_1.18.0         Matrix_1.0-3
>  [4] lattice_0.20-0       limma_3.10.2         RColorBrewer_1.0-5
>  [7] pdInfoBuilder_1.18.0 affxparser_1.26.2    RSQLite_0.11.1
> [10] DBI_0.2-5            ff_2.2-5             bit_1.1-8
> [13] oligo_1.18.1         oligoClasses_1.16.0  Biobase_2.14.0
> [16] stringr_0.6
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.22.0         annotate_1.32.1       AnnotationDbi_1.16.16
>  [4] Biostrings_2.22.0     IRanges_1.12.6        plyr_1.7.1
>  [7] preprocessCore_1.16.0 splines_2.14.1        survival_2.36-12
> [10] xtable_1.7-0          zlibbioc_1.0.0
>
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