Hi Sean, (and others)

Does it usually take an obscenely long time for makeDBPackage to run when
given a bunch of refseq IDs?  I ran the following:

> makeDBPackage("HUMANCHIP_DB", affy=FALSE,
prefix="IlluminaHumanMethylation450k",fileName="acc450k.txt",baseMapType='refseq',version='1.0.0',manufacturer='Illumina',chipName='Human
Methylation 450k', manufacturerUrl='http://illumina.com/')
baseMapType is refseq # time passes...

and it's doing SOMETHING, because the table temp_probe_map in the sqlite
file it created is filling up.  But it's been grinding away at this for the
past 12 hours, which seems a bit excessive for mapping 806,334 refseq
accessions.  Really, all I want is for my bimap objects to work as expected,
the annotation integration is just gravy.

The idea was to release updated 27k and completed 450k packages to handle
the IDAT mappings, immediately followed by a methylumIDAT release, and start
merging that and my preprocessing stuff into the [methy]lumi toolchain.  The
450k probes are split between two designs, so I kind of had to bite the
bullet and roll my own schema to do the mappings efficiently, plus between
450k and FFPE samples there has been a LOT of weirdness lately that I'd like
not to depend on Illumina's software to handle.  So...

I started out doing this on my laptop (gave up after a few hours and moved
it to the server):

> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-12-21 r53879)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
 [1] human.db0_2.4.1                      ChIPpeakAnno_1.7.0

 [3] limma_3.5.20                         GO.db_2.4.1

 [5] BSgenome.Ecoli.NCBI.20080805_1.3.16  BSgenome_1.19.2

 [7] GenomicRanges_1.3.7                  Biostrings_2.19.2

 [9] IRanges_1.9.17                       multtest_2.6.0

[11] biomaRt_2.7.1                        groupedPMA_0.2

[13] betareg_2.2-3                        Formula_1.0-0

[15] PMA_1.0.7                            huge_0.9

[17] MASS_7.3-9                           igraph_0.5.5-1

[19] glasso_1.4                           glmnet_1.5.1

[21] Matrix_0.999375-46                   lattice_0.19-17

[23] grplasso_0.4-2                       impute_1.25.0

[25] rGammaGamma_1.0                      methylumIDAT_0.1

[27] IlluminaHumanMethylation27k.db_1.4.0 org.Hs.eg.db_2.4.6

[29] RSQLite_0.9-4                        DBI_0.2-5

[31] AnnotationDbi_1.13.0                 ggplot2_0.8.9

[33] proto_0.3-8                          lumi_2.3.5

[35] nleqslv_1.8                          matrixStats_0.2.2

[37] R.methodsS3_1.2.1                    gsl_1.9-8

[39] methylumi_1.3.3                      Biobase_2.11.7

[41] gtools_2.6.2                         reshape_0.8.3

[43] plyr_1.4

loaded via a namespace (and not attached):
 [1] affy_1.27.2           affyio_1.17.4         annotate_1.27.1
 [4] digest_0.4.2          hdrcde_2.15           KernSmooth_2.23-4
 [7] lmtest_0.9-27         mgcv_1.7-2            nlme_3.1-97
[10] preprocessCore_1.11.0 RCurl_1.5-0           sandwich_2.2-6
[13] splines_2.13.0        survival_2.36-2       tools_2.13.0
[16] XML_3.2-0             xtable_1.5-6

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