Michael,

Thanks for the diagnosis.

I'm not up on namespaces in R or I would offer to patch.

Meantime, I wonder if there is a workaround....

Guessing, I tried

namespaceImport(asNamespace('GGally'),from=asNamespace('ggplot2'))

but no dice.

Thanks,

Malcolm

From: Michael Lawrence [mailto:lawrence.michael@gene.com]
Sent: Saturday, November 09, 2013 11:38 AM
To: Paulson, Ariel
Cc: Cook, Malcolm; r-discussion@listserv.stowers.org; bioconductor@r-project.org; Tengfei Yin (tengfei.yin@sbgenomics.com); schloerke@gmail.com
Subject: Re: [BioC] GGally ggbio conflict/bug

Couple of problems:

GGally: needs to import(ggplot2)
ggbio: its GGbio object should support $<- (i.e., it should pass through to its ggplot slot)
If either one is fixed, the problem is resolved. But both should be.
Maintainers: ready, set, fix! ;)
Michael

On Fri, Nov 8, 2013 at 3:40 PM, Paulson, Ariel <apa@stowers.org<mailto:apa@stowers.org>> wrote:
Library load order does not affect the phenotype?

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