User: ioannis.vardaxis

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New User
Location:
Norway/Trondheim/NTNU
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3 weeks, 2 days ago
Joined:
1 year ago
Email:
i***************@ntnu.no

Posts by ioannis.vardaxis

<prev • 7 results • page 1 of 1 • next >
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Problem with BiocParallel::bpiterate
... Hey, I am trying to read a paired-end BAM file in chunks using BiocParallel::bpiterate but the iterations never stop, here is what I do:   bamfile=Rsamtools::BamFile(file="myBamFile",index="myBamFile",asMates=TRUE,yieldSize=1000000) snow <- BiocParallel::SnowParam(workers = 4, type = "SOCK") ...
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Comment: C: BiocParallel exporting function?
... Yes for .parallel=TRUE. I have changed the code now to bplapply, the problem is that when I read the instructions for using bplapply, bioconductor states that the BPPARAM argument should be given by the user. So this is where one has to specify which functions to export if I am not wrong. But there ...
written 12 months ago by ioannis.vardaxis10
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BiocParallel exporting function?
... Hi,   I am trying to replace doMC package with BiocParallel and I have some questions:   1: Is there a way of registering a backhead and then use plyr package with parallel=TRUE? I have tried everything but it does not seem to work, then I changed dlply etc with bplapply and everything works, ho ...
biocparallel written 12 months ago by ioannis.vardaxis10
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Question about sumbition process and biocviews
... Hi, When I upload my package to Github does the evaluation process start immediately? Or do I have to ask for it? Furthermore, during the evaluation process do I get feedback about the dependencies of my package etc? I have those in my description file, but maybe they should be placed a little dif ...
biocviews biocparallel github package submission written 12 months ago by ioannis.vardaxis10 • updated 12 months ago by Martin Morgan ♦♦ 20k
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Comment: C: BiocStyle header specification
... Ok thanks. One last question, i try to add email etc in yaml but it doesn't appear on the pdf: --- title: "pkg" author: "author" email: email@.. date: "`r doc_date()`" package: "`r BiocStyle::pkg_ver('pkg')`" output: BiocStyle::pdf_document2 vignette: > %\VignetteIndexEntry{pkg} %\VignetteE ...
written 12 months ago by ioannis.vardaxis10
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Comment: C: BiocStyle header specification
... hi, thanks for the answer. I know, but if I dont do that then i cannot use :\bioctitle[pkg]{long pkg name} and the package will only have a sort name actually i cannot use any of the biocstyle options in the yalm since biocstyle has to be loaded after the yalm. Therefore everythink is doubled. ...
written 12 months ago by ioannis.vardaxis10
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BiocStyle header specification
... Hi, I am trying to use BiocStyle to create vignette in R markdown. I read the instructions but i dont get the results i want so I was wondering what I have done wrong. I dont understand where I should place the first chuck which loads latex2. If i do it this way i get two pages with double author e ...
biocstyle written 12 months ago by ioannis.vardaxis10 • updated 12 months ago by James W. MacDonald45k

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