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hi Dan, On 06/12/2014 04:28 PM, Dan Tenenbaum wrote: [...] > > Thanks for figuring this out and sharing it. > > Note that on the build machines, the compiler used on Mavericks is not gcc but clang. > More info here: > > http...

hi, the performance of snpsByOverlaps() in terms of time and memory consumption is quite poor and i wonder whether there is some bug in the code. here's one example: library(GenomicRanges) library(SNPlocs.Hsapiens.dbSNP144.GRCh37) snps <- SNPlocs.Hsapiens...

hi, I have noticed that in the recent release of BioC the vignettes produced as Sweave/PDF documents do not show anymore the metadata written using %\VignetteIndexEntry{}, while this seems to work fine with the HTML vignettes. compare for instance...

hi, this is a question for limma developers. at every new fresh installation of BioC and limma i get this message when i use 'duplicateCorrelation()': "statmod package required but is not installed" i just install 'statmod' and problem solved. this...

hi, the platform availability shield for the release version of GenomicScores pointing here: https://bioconductor.org/shields/availability/release/GenomicScores.svg is missing, if i look up the same shield for another of my packages, it's there: https://bioconductor...

dear people, i need to code a function in C working in R and receives two R SEXP objects as parameters, where one is a list and another is a vector of integers: void f(SEXP list, SEXP vector) { ... return...

hi, i've just tried a new fresh installation of R 2.12 in my Mac OSX 10.6 laptop and found the following problem: source("http://www.bioconductor.org/biocLite.R") biocLite() [... installs everything apparently without problems ...] library(Biobase...

On 09/21/2012 06:32 PM, Vincent Carey wrote: > On Fri, Sep 21, 2012 at 12:26 PM, Robert Castelo<robert.castelo at upf.edu> wrote: >> hi Martin, >> >> >> On 09/21/2012 05:59 PM, Martin Morgan wrote: >>> >>> On...

Try in a fresh run: remove.packages("BiocInstaller") source("http://bioconductor.org/biocLite.R") cheers, robert. -------- Original message -------- From: Kasper Daniel Hansen <kasperdanielhansen at gmail.com> Date:20/10/2015 16:55 (GMT+01:00) To: bioc-devel at r...

hi, i've had a smooth transition from SVN to git for all the software packages i maintain (thanks for the great documentation!!) and i have the following question. i keep a local git repository for each of my software...

Hi, same experience here with VariantFiltering and BSgenome.Hsapiens.1000genomes.hs37d5: https://bioconductor.org/checkResults/3.22/bioc-LATEST/VariantFiltering/taishan-buildsrc.html robert. On 3/10/25 09:56, Ulrich Bodenhofer wrote: > Dear colleagues, > > Since the release of Bioconductor...

Thanks Herv?, this looks very useful!!! robert. On 03/07/2020 07:49, Herv? Pag?s wrote: > Hi Vince, Robert, Kasper, > > I've done some work on this. Starting with GenomeInfoDb_1.25.7 the > seqlevelsStyle() setter has 2 major...

I second this, and would suggest to name the style as 'GRC' for "Genome Reference Consortium". thanks Vince for bringing this up, being able to easily switch between genome styles is great. if 'paste0()' in R is one of the...

thanks Martin, i'm still getting emails delivered (hundreds in the case of these spam emails) from the support site, even though it's unavailable. would it be possible also to stop the email delivery until the issue is fixed...

hi Koen, you can do some analysis of the dependencies using the BiocPkgTools as follows: library(BiocPkgTools) depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"), dependencies=c("Depends", "Imports")) ## if you get this error ## ## Error in readRDS(gzcon(con)) : ## ? cannot open the...

excellent, thank you so much Lori for following this up. have a nice weekend!! robert. On 21/05/2021 15:10, Kern, Lori wrote: > I'm sorry this took so long to get back to.? ?I have fixed the issue...

Herv?, Martin, Thank you so much, atena builds and checks cleanly now on kunpeng2 too!! https://bioconductor.org/checkResults/3.18/bioc-LATEST/atena cheers, robert. On 10/23/23 20:46, Herv? Pag?s wrote: > > On 10/23/23...

hi, multiple packages, among them, Gviz or VariantFiltering, currently break in the build machines with the following error: Error : object ?path? is not exported by 'namespace:Rsamtools' see, for instance: http://www.bioconductor.org/checkResults/3.7/bioc-LATEST/VariantFiltering...

hi Kasper, you're right. i should have done this upfront, this was too much S4 magic to be true :) cheers, robert. On 1/10/14 5:14 PM, Kasper Daniel Hansen wrote: > Robert: The alternative to using exprs<- is...

great, thanks Lori! robert. On 04/02/2021 20:06, Kern, Lori wrote: > The instructions for updating an experiment data package are the same > as software.? They are located at git.bioconductor.org and have the > same branch structuring for...