[Bioc-devel] Found more than one class "Annotated" in cache

[Michael Lawrence]

Yea, this is a bug in R, in my opinion. The class cache circumvents
the namespace imports. In my working copy I've fixed it by falling
back to the namespace search when there are multiple hits. That at
least fixes this case.

You can disable the message in the short term by setting the
"getClass.msg" option to FALSE.

Michael

On Sun, Apr 24, 2016 at 12:50 PM, davide risso <risso.davide at gmail.com> wrote:
> Dear list,
>
> we are developing a new package that defines a class that builds on
> SummarizedExperiment and also imports the CRAN package phylobase.
>
> The class "Annotated" is defined both in the S4Vectors package (a
> dependency of SummarizedExperiment) and in the RNeXML package (a dependency
> of phylobase). Note that we want the former. This causes the following
> message to be thrown every time we create a new object.
>
> Found more than one class "Annotated" in cache; using the first, from
> namespace 'S4Vectors'
>
>
> A minimal example is the following.
>
>> library(SummarizedExperiment)> SummarizedExperiment()class: SummarizedExperiment
> dim: 0 0
> metadata(0):
> assays(0):
> rownames: NULL
> rowData names(0):
> colnames: NULL
> colData names(0):> library(phylobase)> SummarizedExperiment()Found
> more than one class "Annotated" in cache; using the first, from
> namespace 'S4Vectors'class: SummarizedExperiment
> dim: 0 0
> metadata(0):
> assays(0):
> rownames: NULL
> rowData names(0):
> colnames: NULL
> colData names(0):
>
>> sessionInfo()R Under development (unstable) (2016-03-07 r70284)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux stretch/sid
>
> 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=en_US.UTF-8       LC_NAME=C
> LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils
> datasets  methods
> [9] base
>
> other attached packages:
> [1] phylobase_0.8.2             SummarizedExperiment_1.1.21
> [3] Biobase_2.31.3              GenomicRanges_1.23.23
> [5] GenomeInfoDb_1.7.6          IRanges_2.5.39
> [7] S4Vectors_0.9.41            BiocGenerics_0.17.3
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.3      plyr_1.8.3       XVector_0.11.7   iterators_1.0.8
>  [5] tools_3.3.0      zlibbioc_1.17.0  uuid_0.1-2       jsonlite_0.9.19
>  [9] nlme_3.1-125     lattice_0.20-33  foreach_1.4.3    DBI_0.3.1
> [13] httr_1.1.0       stringr_1.0.0    dplyr_0.4.3      xml2_0.1.2
> [17] ade4_1.7-4       grid_3.3.0       rredlist_0.1.0   reshape_0.8.5
> [21] data.table_1.9.6 R6_2.1.2         XML_3.98-1.4     RNeXML_2.0.6
> [25] reshape2_1.4.1   tidyr_0.4.1      magrittr_1.5     codetools_0.2-14
> [29] assertthat_0.1   bold_0.3.5       taxize_0.7.5     ape_3.4
> [33] stringi_1.0-1    rncl_0.6.0       lazyeval_0.1.10  rotl_0.5.0
> [37] chron_2.3-47
>
>
> Since we need to import both packages, is there a way to explicitly use the
> correct definition of "Annotated" or to not import the class "Annotated"
> from RNeXML?
>
> Or is this something that could be addressed in the SummarizedExperiment
> package?
>
> These are our DESCRIPTION and NAMESPACE file (note that we are importing
> only what we need from phylobase):
> https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
> https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE
>
> See also Henrik's comment at:
> https://github.com/epurdom/clusterExperiment/issues/66
>
> Thank you in advance for any help!
>
> Best,
> davide
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>