urther, the second
entry of .Random.seed is not the same after running setup_create_objects.R on
the devel version as the new version.
Thanks,
Elizabeth Purdom
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htt
especially given that the underlying `data.frame`
allows this call.
Thanks,
Elizabeth Purdom
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No, sorry, it was also a problem with `Matrix` package. I was too quick in
checking it. I think upgrading my devtools and roxygen2 may have fixed it.
Thanks for helping me pinpoint where the problem was.
> On Oct 19, 2018, at 12:37 PM, Elizabeth Purdom
> wrote:
>
> T
Methods("nNodes")
>
> and R/cls.R
>
> .A = setClass("A", slots = c(x="numeric"))
> setMethod("nNodes", "A", function(x) "I'm an 'A'")
>
> This package builds and checks OK (complaining about documentati
Sorry, I copied the wrong code from phylobase (I copied the setMethod code).
Their setGeneric calls are in the following format:
setGeneric("nNodes", function(x) {
standardGeneric("nNodes")
})
> On Oct 19, 2018, at 9:07 AM, Elizabeth Purdom
> wrote:
>
Hello,
In my package (`clusterExperiment`) I want to extend a S4 method from a package
`phylobase` for my class. However, in the phylobase package, all of the
`setGeneric` calls are in the form of
setMethod("nTips", signature(x="phylo"),
function(x) {
Ntip(x)
})
Namely, they use braces
(though if so, I’d say the
>> warning is awfully cryptic, especially since it says to use `setClassUnion`
>> as a solution). In my other cases, I have just gone ahead and imported all
>> of the subclasses from the package that defines the memb
ees this generally. But given that we’re coming up on a
release I thought I would ask if there’s anything I can do to get rid of this
warning! Or can I go with my first instinct and safely ignore it?
Thanks,
Elizabeth Purdom
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gt;>>
>>> On Mon, Apr 30, 2018 at 11:28 AM, Martin Morgan <
>>> martin.mor...@roswellpark.org> wrote:
>>>
>>>> But that issue will be fixed, so Tim's advice is inappropriate.
>>>>
>>>>
>>>> On 04/30/2018 10:42 AM
Hello,
I am trying to extend my package to handle `HDF5Matrix` class ( or more
generally `DelayedArray`). I currently have S4 functions for `matrix` class.
Usually I have a method for `SummarizedExperiment`, which will call call the
method on `assay(x)` and I want the method to be able to deal
e calling package as the fallback, so
>>>>>>>> DataFrame(1:5) no longer produces a message. But calling it from
>>>>>>>> another package, or global env, will still break, just like new().
>>>>>>>> How
>>>>>>>> d
ave S4Vectors_0.17.42 while I am working with
> 0.17.41.
> On a linux system this error was not thrown.
>
>
> On Tue, Apr 17, 2018 at 6:14 AM, Elizabeth Purdom <epur...@stat.berkeley.edu
> <mailto:epur...@stat.berkeley.edu>> wrote:
> Hello,
>
>
ase I am also wondering if I should roll back to an
earlier version for now, and if so which one so that I’m still reasonably
current?
Thanks,
Elizabeth Purdom
Following example from the help pages of saveHDF5SummarizedExperiment:
> library(HDF5Array)
> library(SummarizedExperiment)
>
tidyr_0.8.0
> reshape2_1.4.3
> [37] magrittr_1.5 codetools_0.2-15 assertthat_0.2.0
> bold_0.5.0
> [41] taxize_0.9.3 stringi_1.1.7 lazyeval_0.2.1
> RCurl_1.95-4.10
> [45] zoo_1.8-1
>
that in development version 2018-03-22 r74446, where I was able to
install all of the packages, I was not getting these messages.
Thanks,
Elizabeth Purdom
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https://s
ve you what you want?
>
> On Wed, 4 Apr 2018 at 14:58 Elizabeth Purdom <epur...@stat.berkeley.edu
> <mailto:epur...@stat.berkeley.edu>> wrote:
> Hello,
>
> I am trying to do a rbind a normal (in memory) matrix with a HDF5Matrix
> object or DelayedA
into a DelayedMatrix object in
order to do rbind.
Thanks,
Elizabeth Purdom
Here is my code setting up the objects:
> testdata<-matrix(rnorm(1000),nrow=100,ncol=10)
> testhdf<-HDF5Array::writeHDF5Array(testdata, "./trash.h5")
> class(testhdf)
[1] "HDF5Matrix"
attr(,"packag
sterings of single-cell sequencing data or other large mRNA
Expression data sets.
Authors@R: c(person("Elizabeth", "Purdom", email = "epur...@stat.berkeley.edu",
role = c("aut", "cre", "cph")),
person("
rast" "Node" "isMerged" "mergeClusterId"
Thank you very much for your help in getting an interactive session in the
build environment!
Elizabeth
> On Oct 23, 2017, at 4:35 PM, Martin Morgan <martin.mor...@roswellpark.org>
> wrote:
>
>
> I can reproduce the error with
>
> clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C R -f
> clusterExperimentTutorial.R
>
> leading to
>
> > ##
> > recallRSEC
> >
> On Oct 23, 2017, at 3:47 PM, Martin Morgan <martin.mor...@roswellpark.org>
> wrote:
>
> On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:
>> Hello,
>> I am updating an existing package and I am getting an error in running my
>> vignette (and a simil
unclear how it
would be a namespace error.
Thanks for any suggestions,
Elizabeth Purdom
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