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

[mabawsa]

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