sqliteSendQuery(con, statement, bind.data) error using makePdInfoPackage for Nimblegen array
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zenekzkk • 0
Last seen 5.9 years ago


I am trying to use makePdInfoPackage to build an annotation package for Nimblegen Tiling array. I was following the "Building Annotation Packages with pdInfoBuilder for Use with the oligo Package" pdf and I encountered a problem that I can't solve. Below is my code:


baseDir <- "/path/to/dir"
ndf <- list.files(baseDir, pattern = ".ndf", full.names = TRUE)
xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]
pos <- list.files(baseDir, pattern = ".pos", full.names = TRU

seed <- new("NgsTilingPDInfoPkgSeed",
        ndfFile = ndf, xysFile = xys,
        posFile = pos, author = "Name",
        email = "email",
        biocViews = "AnnotationData",
        genomebuild = "unspecified", organism = "unspecified",
        species = "unspecified")

makePdInfoPackage(seed, destDir = ".")

This is the error:

Building annotation package for Nimblegen Tiling Array
NDF: 121115_Eco_T4_PG_expr.ndf
POS: 121115_Eco_T4_PG_expr.pos
XYS: 558928_CTRL1_A01_2013-12-20_532.xys
Parsing file: 121115_Eco_T4_PG_expr.ndf... OK
Parsing file: 121115_Eco_T4_PG_expr.pos... OK
Merging NDF and POS files... OK
Parsing file: 558928_CTRL1_A01_2013-12-20_532.xys... OK
Creating package in ./pd.121115.eco.t4.pg.expr 
Inserting 8090 rows into table featureSet... OK
Inserting 99298 rows into table pmfeature... OK
Inserting 0 rows into table bgfeature... Error in sqliteSendQuery(con, statement, bind.data) : 
  bind.data must have non-zero dimensions

I looked it up in the internet but found very little useful information for me. Any hint will be much appreciated. Below is my sessionInfo()

R version 3.2.1 (2015-06-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.10

 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=pl_PL.UTF-8           LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=pl_PL.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=pl_PL.UTF-8          LC_NAME=pl_PL.UTF-8          
 [9] LC_ADDRESS=pl_PL.UTF-8        LC_TELEPHONE=pl_PL.UTF-8     

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] pdInfoBuilder_1.32.1 affxparser_1.40.0    RSQLite_1.0.0       
 [4] DBI_0.3.1            oligo_1.32.0         Biostrings_2.36.3   
 [7] XVector_0.8.0        IRanges_2.2.7        S4Vectors_0.6.3     
[10] oligoClasses_1.30.0  HELP_1.26.0          Biobase_2.28.0      
[13] BiocGenerics_0.14.0  rj_2.0.4-2          

loaded via a namespace (and not attached):
 [1] splines_3.2.1         GenomicRanges_1.20.5  zlibbioc_1.14.0      
 [4] bit_1.1-12            rj.gd_2.0.0-1         foreach_1.4.2        
 [7] GenomeInfoDb_1.4.2    tools_3.2.1           ff_2.2-13            
[10] iterators_1.0.7       preprocessCore_1.30.0 affyio_1.36.0        
[13] codetools_0.2-14      BiocInstaller_1.18.4 


microarray R oligo micro array data annotation • 732 views

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