Thank you! After updating the package, the problem is solved. On Wed, Oct 30, 2013 at 4:35 AM, Kasper Daniel Hansen <khansen@jhsph.edu>wrote: > 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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]