Hi list,

This wasn't sent out with a none registered ids. I have a problem with
forging a new BSgenome data package. The sequence data file is clof.v3.fa
and the mask file is clof.v3.fa.masked. Below are seed file, command, error
and sessioninfo. Your help will be much appreciated.

Thanks a lot,
Steve

Package: BSgenome.Clof.yu.v3
Title: Clof (insects) full genome (version 3)
Description: Clof (insects) full genome as provided by YU (V3.3, Jan. 2011)
# and will store in Biostrings objects.
Version: 1.0.0
organism: clof
species: insect
provider: YU
provider_version: Assembly V3.3
release_date: Jan, 2011
release_name: insects Genome Reference Consortium
source_url: NA # http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
organism_biocview: Clof
BSgenomeObjname: Clof
seqnames: "clof_v3.fa"
mseqnames: NA #paste("upstream", c("1000", "2000", "5000"), sep="")
nmask_per_seq: 2
#SrcDataFiles1: sequences: chromFa.zip, upstream1000.zip, upstream2000.zip,
upstream5000.zip
    #from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
#SrcDataFiles2: AGAPS masks:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz
    #RM masks:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromOut.tar.gz
    #TRF masks:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromTrf.tar.gz
PkgExamples: Hsapiens
    seqlengths(Hsapiens)
    Hsapiens$chr1  # same as Hsapiens[["chr1"]]
seqs_srcdir: /home/steve/Data/Genomes
masks_srcdir: /home/steve/Data/Genomes
AGAPSfiles_name: clof_v3.fa.masked

The command, error and sessionInfo are below

> forgeBSgenomeDataPkg("Clof_seed.R", seqs_srcdir=".", masks_srcdir=".",
destdir=".", verbose=TRUE)
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.


Attaching package: 'Biobase'

The following object(s) are masked from 'package:IRanges':

    updateObject

Error in forgeBSgenomeDataPkg(y, seqs_srcdir = seqs_srcdir, masks_srcdir =
masks_srcdir,  :
  values for symbols NMASKPERSEQ are not single strings
In addition: Warning message:
In storage.mode(x$nmask_per_seq) <- "integer" : NAs introduced by coercion
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Biobase_2.6.1       BSgenome_1.18.2     Biostrings_2.18.0
[4] GenomicRanges_1.2.1 IRanges_1.8.8

loaded via a namespace (and not attached):
[1] tools_2.12.1

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