Our core has produced raw lumi output for me that includes these  
annotation columns:

[51] "SEARCH_KEY"                   "UNIGENE_ID"
[53] "ENTREZ_GENE_ID"               "ACCESSION"
[55] "SYMBOL"                       "PROBE_ID"
[57] "DEFINITION"                   "X"

  lumiR reads the following annotation columns:

ACCESSION, SYMBOL,
PROBE START, CHROMOSOME, PROBE CHR ORIENTATION, PROBE COORDINATES,
DEFINITION.

Perhaps since these are not there, I get this message:

Please provide the annotation file or lumi annotation library!

What is unclear to me, having read the lumi documentation, is whether  
I can
avoid this message by just adding bioconductor annotations in. I tried  
it like this

 > data <- lumiR("FinalReport.txt", lib.mapping = "lumiHumanIDMapping")

Warning message:
In addNuID2lumi(x.lumi, lib.mapping = lib.mapping) :
   More than 500 identifiers cannot be found in the  
library:lumiHumanIDMapping!
  The provided library might be wrong or outdated!


 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] lumiHumanIDMapping_1.8.0 RSQLite_0.9-4            DBI_0.2-5
[4] AnnotationDbi_1.12.0     lumi_2.2.0               Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] affy_1.28.0           affyio_1.18.0         annotate_1.28.0
  [4] grid_2.12.0           hdrcde_2.15           KernSmooth_2.23-4
  [7] lattice_0.19-13       MASS_7.3-8            Matrix_0.999375-44
[10] methylumi_1.6.1       mgcv_1.6-2            nlme_3.1-97
[13] preprocessCore_1.12.0 tcltk_2.12.0          xtable_1.5-6



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