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

[davide risso]

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]]