On 04/25/2016 03:53 PM, Michael Lawrence wrote:
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.
This also fixes it
Index: src/library/methods/R/SClasses.R
===================================================================
--- src/library/methods/R/SClasses.R (revision 70547)
+++ src/library/methods/R/SClasses.R (working copy)
@@ -524,7 +524,7 @@
superClass <- exti@superClass
if(!exti@simple && !is(object, superClass))
next ## skip conditional relations that don't hold for this object
- superDef <- getClassDef(superClass, where = where)
+ superDef <- getClassDef(superClass, package = packageSlot(exti))
if(is.null(superDef)) {
errors <- c(errors,
paste0("superclass \"", superClass,
There's another problem seen by loading the packages in reverse order
> suppressPackageStartupMessages({ library(RNeXML);
library(GenomicRanges) })
Found more than one class "Annotated" in cache; using the first, from
namespace 'RNeXML'
Also defined by 'S4Vectors'
...
which is from
[[17]]
S4Vectors:::setDefaultSlotValue("XRaw", "shared", new("SharedRaw"),
where = asNamespace(pkgname))
[[18]]
resetClass(classname, classdef, where = where)
[[19]]
completeClassDefinition(Class, classDef, where)
[[20]]
.completeClassSlots(ClassDef, where)
[[21]]
isClass(eClass, where = where)
[[22]]
getClassDef(Class, where)
[[23]]
.getClassFromCache(Class, where, package = package, resolve.msg =
resolve.msg)
but I haven't quite got to the bottom of that. Also, I think these are
both different from but related to
> suppressPackageStartupMessages(library(Statomica))
Error in .mergeMethodsTable(generic, mtable, tt, attach) :
trying to get slot "defined" from an object of a basic class ("list")
with no slots
Error: package or namespace load failed for 'Statomica'
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.dav...@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
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