Re: [Bioc-devel] SummarizedExperiments not equal after serialisation

I would say it's much worse than mismatching class definitions. https://github.com/Bioconductor/SummarizedExperiment/issues/16 -A On 5/11/19 5:07 AM, Martin Morgan wrote: I think it has to do with the use of reference classes in the assay slot, which have different environments se = Summa

Re: [Bioc-devel] Pre-receive hook on git.bioconductor.org to prevent merge conflict markers enabled

I worked around this by replacing my = lines with lines. Note that you cannot exclude the possibility that legit code contains things like === or <<< so whatever regex the hook is using at the moment should probably be made more stringent in order to avoid these false positi

Re: [Bioc-devel] Pre-receive hook on git.bioconductor.org to prevent merge conflict markers enabled

Hi Nitesh, I'm running into some problems today when trying to push a commit to BiocGenerics: hpages@spectre:~/git.bioconductor.org/software/BiocGenerics$ git remote -v origin g...@git.bioconductor.org:packages/BiocGe

Re: [Bioc-devel] SummarizedExperiments not equal after serialisation

I think it has to do with the use of reference classes in the assay slot, which have different environments se = SummarizedExperiment() saveRDS(se, fl <- tempfile()) se1 = readRDS(fl) and then > all.equal(se@assays, se1@assays) [1] "Class definitions are not identical" > all.equal(se@assa

[Bioc-devel] SummarizedExperiments not equal after serialisation

I would appreciate some background about the following: > suppressPackageStartupMessages(library("SummarizedExperiment")) > set.seed(1L) > m <- matrix(rnorm(16), ncol = 4, dimnames = list(letters[1:4], LETTERS[1:4])) > rowdata <- DataFrame(X = 1:4, row.names = letters[1:4]) > se1 <- SummarizedExpe