[Bioc-devel] loading VariantAnnotation package breaks ggplot2::qplot when faceting, potential cbind problem?

[Martin Morgan]

On 9/12/2012 3:42 PM, Tengfei Yin wrote:
>
>
> On Wed, Sep 12, 2012 at 5:09 PM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> 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  <http://pmax.int>, pmin,pmin.int  <http://pmin.int>, Position, rbind, Reduce,rep.int  <http://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  <http://rep.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, ...))
>     <environment: namespace:base>
>      > 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.

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 at r-project.org  <mailto:Bioc-devel at 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