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hi, currently the BioC AMI has root partition of 40 Gbytes, is it possible for a user, e.g. me!, to copy rebuild that AMI into a larger volume of, for instance, 100 Gbytes. thanks! robert.

Hi, I'd like to update the experiment data package https://bioconductor.org/packages/GSVAdata but i haven't been able to find instructions in the Bioconductor website. how do i proceed? thanks! robert. -- Robert Castelo, PhD Associate Professor Dept...

Martin, a question regarding this issue just when through my mind, On Wed, 2010-07-21 at 19:20 -0700, Martin Morgan wrote: [...] > An experiment data package is additional work, but in exchange you get > reproducible, reliable, and documented research...

hi, our package atena fails to build **only** in kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64: https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx/kunpeng2-buildsrc.html concretely, the vignette fails to find a BAM file downloaded via...

On Mon, 2010-09-06 at 22:41 -0700, Martin Morgan wrote: [...] > > * checking for file ?qpgraph/DESCRIPTION? ... OK > > * preparing ?qpgraph?: > > * checking DESCRIPTION meta-information ... OK > > * cleaning src > > * running cleanup > > * installing the package to process help pages > > * building the package manual...

hi, i'm interested in having classes 'VcfFile' and 'VcfFileList', analogous to 'BamFile'/'BamFileList' or 'Bcf/BcfFileList,' with their corresponding functionality to ease manipulating, in this case, VCF files. i thought i could sort of copy&paste code from Rsamtools...

hi, on tuesday april 11th i checked in changes for VariantFiltering version 1.11.10 and i've seen that today the build for tuesday gives errors on version 1.11.9 with snapshot date from april 7th. i do...

hi, i'm using the CompressedVRangesList class in VariantFiltering to hold variants and their annotations across multiple samples and found that there was no show method for this class (unless i'm missing the right import here) so i made...

hi, the 'BiocParallel::bpiterate()' method shows progress through the following call: setMethod("bpiterate", c("ANY", "ANY", "SerialParam"), ??? function(ITER, FUN, ..., REDUCE, init, reduce.in.order = FALSE, ??????? BPPARAM=bpparam()) { [...] ??? progress <- .progress(active=bpprogressbar(BPPARAM), iterate=TRUE) [...] } where the argument 'iterate=TRUE...

oops, sorry, I can clone, pull and push, just pinging doesn't work, it must be a problem on your end. robert. On 10/27/25 17:04, Johannes Rainer wrote: > Hi all, > > just to make sure it's not...

Hi, i submitted one release ago the following annotation packages: MafDb.ALL.wgs.phase1.release.v3.20101123 MafDb.ESP6500SI.V2.SSA137.dbSNP138 phastCons100way.UCSC.hg19 for which i'm also the "maintainer". while the functionality to access their annotation resides...

Same here, $ ping git.bioconductor.org PING git.bioconductor.org (34.192.48.227) 56(84) bytes of data. robert. On 10/27/25 17:04, Johannes Rainer wrote: > Hi all, > > just to make sure it's not me or...

dear developers, i'm adding parallel support to my package by copying & pasting the way in which this is done by other packages like ShortRead. i'm currently using 'snow' and since i'm providing this support for computing-intensive...

hi Martin, On 09/21/2012 05:59 PM, Martin Morgan wrote: > On 09/21/2012 05:05 AM, Benilton Carvalho wrote: >> Replace >> >> Biobase::`annotation<-`(eScoEset, "") >> >> by >> >> Biobase::`annotation<-`(eScoEset, value="") > > why not just > > annotation(eScoEset) <- "" > > with importFrom(Biobase, "annotation...

Dear Fursham, sure, we add resources either when we need them ourselves or when our users request them. could you please open an issue with the request at https://github.com/rcastelo/GenomicScores/issues ?? thanks, robert. On 06/05/2022...

hi, i have just noticed that VariantFiltering breaks in the last build: http://www.bioconductor.org/checkResults/3.1/bioc-LATEST/VariantFiltering/zin2-buildsrc.html and the reason is that the devel annotation package http://www.bioconductor.org/packages/devel...

hi Martin, On Wed, 2012-03-14 at 15:58 -0700, Martin Morgan wrote: [...] > So the answer to the original post should have been closer to 'use > EntrezIdentifier for org.Hs.eg.db annotations'? As in the final line of...

hi, currently, the annotation of variants in intronic regions by VariantAnnotation and the locateVariants() function does not assign strand to annotations in introns: library(VariantAnnotation) example(locateVariants) loc_all[loc_all$LOCATION == "intron"] GRanges object with 2 ranges and 9...