That code is executed when the package is being build on the build server -
ie. it runs on the build server.  Having said that, I vaguely recalling
seeing this error before.

I see you are running an old version of bsseq though, so I would suggest
updating to the newest Bioconductor release, and also checking using
  biocValid()
that all your packages are the right version.  If you still get the error
after doing this, you should report back

Best,
Kasper


On Tue, Oct 29, 2013 at 7:52 PM, genefan [guest] <guest@bioconductor.org>wrote:

>
> dear all,
>
> I was trying to apply dmrFinder function in bsseq package, but it always
> gives the following error:
>
> ##################################################
> dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6))
> segmenting
> splitting
> creating dmr data.frame
> Error in ifelse(regions$meanDiff > 0, "hyper", "hypo") :
>   error in evaluating the argument 'test' in selecting a method for
> function 'ifelse': Error in regions$meanDiff : $ operator is invalid for
> atomic vectors
> ##################################################
> The code is from
> http://www.bioconductor.org/packages/2.13/bioc/vignettes/bsseq/inst/doc/bsseq_analysis.R
>
> Thank you for any solution!
> best,
> Jun
>
>  -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-suse-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
>  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
>  LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] bsseqData_0.1.3      bsseq_0.8.0          matrixStats_0.8.5
>  GenomicRanges_1.12.4
> [5] IRanges_1.18.2       BiocGenerics_0.6.0   BiocInstaller_1.10.4
> seqinr_3.0-7
>
> loaded via a namespace (and not attached):
>  [1] Biobase_2.20.1     colorspace_1.2-4   dichromat_2.0-0    grid_3.0.1
>       labeling_0.2
>  [6] lattice_0.20-15    locfit_1.5-9.1     munsell_0.4.2      plyr_1.8
>       RColorBrewer_1.0-5
> [11] R.methodsS3_1.5.2  scales_0.2.3       stats4_3.0.1
> stringr_0.6.2      tools_3.0.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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