Hi

Sorry that it turn out somehow the package in my repos is broken even though
I call svn update it doesn't work, UseDynLib is missing... it's actually in
the svn of GenomicRanges, I just clean the  repos and check out again, it
works now.

Regards

Tengfei

On Mon, Aug 8, 2011 at 2:02 PM, Tengfei Yin <yintengfei@gmail.com> wrote:

> Dear all,
>
> I just tried to run the example under "readGappedAlignments" from
> Rsamtools, and get an error message as shown below, I am using the latest R
> and Rsamtools/GenomicRanges, is it because the dynamic loading is not in the
> NAMESPACE of GenomicRanges?
>
> Thanks in advance!
>
> Tengfei
>
> ###########################
>
> > library(Rsamtools)  # because file ex1.bam is in this package
> Loading required package: IRanges
>
> Attaching package: ‘IRanges’
>
> The following object(s) are masked from ‘package:base’:
>
>     cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
>     pmin, pmin.int, rbind, rep.int, setdiff, table, union
>
> Loading required package: GenomicRanges
> Loading required package: Biostrings
> > galn_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
> > galn <- readGappedAlignments(galn_file)
> Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
>   C symbol name "valid_cigar" not in DLL for package "GenomicRanges"
> > sessionInfo()
> R Under development (unstable) (2011-08-08 r56671)
> 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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Rsamtools_1.5.46     Biostrings_2.21.6    GenomicRanges_1.5.22
> [4] IRanges_1.11.18
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.21.3    RCurl_1.6-0        rtracklayer_1.13.0 XML_3.4-0
>
> [5] zlibbioc_0.1.7
>
>
> ################################################
>
>
>
> --
> Tengfei Yin
> MCDB PhD student
> 1620 Howe Hall, 2274,
> Iowa State University
> Ames, IA,50011-2274
> Homepage: www.tengfei.name
>
>
>


-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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