[BioC] makePdInfoPackage failure

[John O. Woods]

I'm getting a strange error (see below). I also tried the Harvard
bpmaps for NCBIv36, but they give a different error.

Code:

library(pdInfoBuilder)

# symbolically linked from ~/LabNotebook/, actually in /work/jwoods/
subdirs on Einstein.
# bpmapFile <- "Hs35b_P01R_v01-3_NCBIv36.NR.bpmap" # Harvard version

# Harvard version appears to not work with the Affy cif. Need a
different cif from
# somewhere.

bpmapFile <- "Hs35b_P01R_v01-3_NCBIv34.bpmap" # Affy version
cifFile <- "Hs35b_P01R_v01.cif"

obj <- new("AffyTilingPDInfoPkgSeed",
           version="0.0.1",
           author="John O. Woods",
           email="john.woods at mail.utexas.edu",
           biocViews="AnnotationData",
           genomebuild="NCBI Build 34",
           bpmapFile=bpmapFile,
           cifFile=cifFile)

makePdInfoPackage(obj, destDir="/work/jwoods/pd-packages")


Error message for Affy bpmaps:

Creating package in /work/jwoods/pd-packages/pd.hs35b.p01r.v01.3.ncbiv34
Error in rbind(cbind(do.call(cbind, u[cols.pm]), atom = 1:length(u[[2]]),  :
  number of columns of matrices must match (see arg 2)
Timing stopped at: 22.73 0.576 23.331
>


Alternatively, the error message for the Harvard bpmaps:

Creating package in /work/jwoods/pd.hs35b.p01r.v01.3.ncbiv36.nr
Error in sqliteExecStatement(conn, statement, bind.data, ...) :
  RS-DBI driver: (RS_SQLite_exec: could not execute: PRIMARY KEY must be unique)
Timing stopped at: 14.441 0.14 14.577


This is all for the Affy human tiling array.

Thoughts?

Thanks,
John