[BioC] GGally ggbio conflict/bug

[Paulson, Ariel]

Library load order does not affect the phenotype?

-----Original Message-----
From: r-discussion-bounces at listserv.stowers.org [mailto:r-discussion-bounces at listserv.stowers.org] On Behalf Of Cook, Malcolm
Sent: Friday, November 08, 2013 5:09 PM
To: 'r-discussion at listserv.stowers.org'; 'bioconductor at r-project.org'; 'Tengfei Yin (tengfei.yin at sbgenomics.com)'; 'schloerke at gmail.com'
Subject: [R-discussion] GGally ggbio conflict/bug

H'lo fellow and prospective users of R libraries GGally/ggbio, both stupendous extensions to the ggplot library,

I have an unfortunate interaction to report.... 

In my hands, loading ggbio on top of GGally causes GGally examples to fail.

look see:

> library(GGally)
Loading required package: ggplot2
Loading required package: reshape
Loading required package: plyr

Attaching package: 'reshape'

The following objects are masked from 'package:plyr':

    rename, round_any

Warning messages:
1: replacing previous import by 'reshape::rename' when loading 'GGally' 
2: replacing previous import by 'reshape::round_any' when loading 'GGally' 

>example(ggpairs)
# output excised ...
>pm                    # the plot is pretty

# now load the other library:
>library(ggbio)

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim

> pm                # but now I don't get to see the plot because:
Error in `$<-`(`*tmp*`, "type", value = "diag") : 
  no method for assigning subsets of this S4 class
>

My workaround is ... erhm ...egad ...

... don't use ggbio, which, due to other issues with current release (reported seperatlely) I have most unfortunately stopped using anyway.

Thanks!

What else?

~Malcolm Cook


PS. oh, yeah:

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] ggbio_1.10.0    GGally_0.4.4    reshape_0.8.4   plyr_1.8        ggplot2_0.9.3.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.24.0    Biobase_2.22.0          BiocGenerics_0.8.0      biomaRt_2.18.0          Biostrings_2.30.0       biovizBase_1.10.0       bitops_1.0-6            BSgenome_1.30.0         cluster_1.14.4          colorspace_1.2-4        DBI_0.2-7               dichromat_2.0-0         digest_0.6.3            GenomicFeatures_1.14.0  GenomicRanges_1.14.3    grid_3.0.2              gridExtra_0.9.1         gtable_0.1.2            Hmisc_3.12-2            IRanges_1.20.4          labeling_0.2            lattice_0.20-24         MASS_7.3-29             munsell_0.4.2          
[25] parallel_3.0.2          proto_0.3-10            RColorBrewer_1.0-5      RCurl_1.95-4.1          reshape2_1.2.2          rpart_4.1-3             Rsamtools_1.14.1        RSQLite_0.11.4          rtracklayer_1.22.0      scales_0.2.3            stats4_3.0.2            stringr_0.6.2           tools_3.0.2             VariantAnnotation_1.8.2 XML_3.98-1.1            XVector_0.2.0           zlibbioc_1.8.0         
>

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