On Wed, Sep 12, 2012 at 5:48 PM, Martin Morgan wrote: > On 9/12/2012 3:42 PM, Tengfei Yin wrote: > >> >> >> On Wed, Sep 12, 2012 at 5:09 PM, Martin Morgan > > wrote: >> >> On 9/12/2012 1:47 PM, Tengfei Yin wrote: >> >>> Dear developers, >>> >>> I hit some problem I am not able to fix or find what's really going >>> on. >>> When I simply import VCF class in namespace, that will break >>> ggplot2::qplot >>> function when faceting turns on, at first I thought it's ggbio's >>> problem, >>> but when I dig into it, looks like, the cbind function used inside >>> ggplot2 >>> changed, looks like ggplot2 suppose to use base::cbind, but use >>> methods:::cbind after loading VariantAnnotation. But maybe I am >>> digging in >>> the wrong direction. >>> >>> Following code demonstrate when loading VariantAnnotation, ggplot2 >>> cannot >>> faceting, even though I import only VCF class in a minimal package, >>> and >>> make the package depends on methods and ggplot2(0.9.2), the same >>> issue >>> still exists, not sure if I am posting in the right place or not. >>> Please >>> let me know if I should post this in somewhere else, thanks. >>> >>> library(ggplot2) >>>> qplot(x = mpg, y = cyl, data = mtcars, facets = . ~ cyl) >>>> library(VariantAnnotation) >>>> >>> Loading required package: GenomicRanges >>> Loading required package: BiocGenerics >>> >>> Attaching package: ‘BiocGenerics’ >>> >>> The following object(s) are masked from ‘package:stats’: >>> >>> xtabs >>> >>> The following object(s) are masked from ‘package:base’: >>> >>> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, >>> get, intersect, lapply, Map, mapply, mget, order, paste, pmax, >>> pmax.int , pmin,pmin.int , >>> Position, rbind, Reduce,rep.int , >>> >>> rownames, sapply, setdiff, table, tapply, union, unique >>> >>> Loading required package: IRanges >>> Loading required package: Rsamtools >>> Loading required package: Biostrings >>> >>>> qplot(x = mpg, y = cyl, data = mtcars, facets = . ~ cyl) >>>> >>> Error inrep.int ("", ncol(r)) : incorrect type for >>> second argument >>> >> >> Wow this is baroque. A simplification of the problem is >> >> > base::cbind >> function (..., deparse.level = 1) >> .Internal(cbind(deparse.level, ...)) >> >> > library(snpStats) >> > head(base::cbind) >> >> 1 function (..., deparse.level = 1) >> 2 { >> 3 na <- nargs() - (!missing(deparse.level)) >> 4 deparse.level <- as.integer(deparse.level) >> 5 stopifnot(0 <= deparse.level, deparse.level <= 2) >> 6 argl <- list(...) >> >> snpStats (which VariantAnnotation Imports:) uses 'cbind2' and >> methods:::bind_activation. bind_activation changes the definition of >> cbind. I think this is a left-over from a time when methods could >> not be written on ... . I'll try and get some clarification from >> R-devel. >> >> >> Hi Martin, >> >> Thanks a lot for the quick reply and the clarification, by the way, is >> there any workaround for this release of Bioconductor, if I want to >> import VariantAnnotation and at the same time use ggplot2 as usual? >> > > It will be fixed up-stream, probably in the next day or two. A dueling > packages approach is to methods:::bind_activation(**FALSE) after your > dependencies are loaded (e.g., in .onLoad()) but there's really no need for > that. > I see, thanks again! Tengfei > > Martin > > >> Thanks >> >> Tengfei >> >> >> Martin >> >> >> sessionInfo() >>>> >>> R version 2.15.1 (2012-06-22) >>> 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=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] ggplot2_0.9.2 VariantAnnotation_1.3.18 >>> Rsamtools_1.9.26 >>> >>> [4] Biostrings_2.25.10 GenomicRanges_1.9.47 IRanges_1.15.34 >>> >>> [7] BiocGenerics_0.3.1 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.19.28 Biobase_2.17.6 biomaRt_2.13.2 >>> [4] bitops_1.0-4.1 BSgenome_1.25.6 colorspace_1.1-1 >>> [7] DBI_0.2-5 dichromat_1.2-4 digest_0.5.1 >>> [10] GenomicFeatures_1.9.29 grid_2.15.1 gtable_0.1.1 >>> [13] labeling_0.1 lattice_0.20-6 MASS_7.3-20 >>> [16] Matrix_1.0-6 memoise_0.1 munsell_0.3 >>> [19] plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 >>> [22] RCurl_1.91-1 reshape2_1.2.1 RSQLite_0.11.1 >>> [25] rtracklayer_1.17.17 scales_0.2.2 snpStats_1.7.3 >>> [28] splines_2.15.1 stats4_2.15.1 stringr_0.6.1 >>> [31] survival_2.36-14 tools_2.15.1 XML_3.9-4 >>> [34] zlibbioc_1.3.0 >>> Thanks a lot >>> >>> Tengfei >>> >>> >>> ______________________________**_________________ >>> Bioc-devel@r-project.org > >>> mailing list >>> https://stat.ethz.ch/mailman/**listinfo/bioc-devel >>> >> >> >> -- >> Dr. Martin Morgan, PhD >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> >> >> >> -- >> Tengfei Yin >> MCDB PhD student >> 1620 Howe Hall, 2274, >> Iowa State University >> Ames, IA,50011-2274 >> >> >> >> > > -- > Dr. Martin Morgan, PhD > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 [[alternative HTML version deleted]]