Dear all,

I am trying to build a txdb object from gff3 for soybean data and try to
make it a package. Code used like this

gmax189 <- makeTranscriptDbFromGFF("~/Gmax_189_gene_exons.gff3",
                                   format = "gff3", species = "Glycine max",
                                   dataSource = "http://www.phytozome.org/")
makeTxDbPackage(txdb = gmax189,
                version = "0.9.1",
                maintainer = "Tengfei Yin",
                author = "Tengfei Yin",
                destDir=".",
                license="Artistic-2.0")

Error message:
Error in gsub("_", "", pkgName) :
  error in evaluating the argument 'x' in selecting a method for function
'gsub': Error: object 'pkgName' not found


Looks like my dataSource should be either BioMart or UCSC, otherwise no
pkgname will be produced in function .makePackageName?

Or should I build annotation package in some other ways?

Thanks a lot

Tengfei

my sessionInfo

> sessionInfo()
R Under development (unstable) (2013-01-21 r61728)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GenomicFeatures_1.11.8 AnnotationDbi_1.21.10  Biobase_2.19.2
[4] GenomicRanges_1.11.28  IRanges_1.17.31        BiocGenerics_0.5.6

loaded via a namespace (and not attached):
 [1] biomaRt_2.15.0     Biostrings_2.27.10 bitops_1.0-5
BSgenome_1.27.1
 [5] DBI_0.2-5          RCurl_1.95-3       Rsamtools_1.11.15
 RSQLite_0.11.2
 [9] rtracklayer_1.19.9 stats4_3.0.0       tools_3.0.0        XML_3.95-0.1

[13] zlibbioc_1.5.0
>



-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274

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