[Bioc-devel] limma Suggests:statmod vs Imports:statmod

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, however, triggers questions from some of

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

Dear Pijush, Once a package has been accepted to Bioconductor, a copy is made in Bioconductor's own git repository and this is the source from which the packages are made available to users. Any change you make in Github won't be automatically reflected there, you have to explicitly make the chan

[Bioc-devel] Unexpected Warning About Cross-Reference Without Package Specification

Good day, I have documented a parameter that is linked to lmFit's documentation. \item{...}{Optional settings that are passed to \code{\link{lmFit}}.} The package checking process displays a warning. * checking Rd cross-references ... WARNING Missing link or links in documentation object 'limma

Re: [Bioc-devel] BioC 2018 poster / talk / scholarship / workshop application deadline May 17

Dear Martin Morgan, I have successfully added the SSH key in github account and Bioconductor. After rechecking the package in Bioconductor I have found that there is a mistake in the DESCRIPTION file. In the Description portion inside the DESCRIPTION file, there are words " Bayesian T statistic",

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

As Herve also indicated already, your best shot is the R-SIG-Debian list for questions on debian like systems. That said, the maintainer Michael Rutter announced the 3.5 binaries for all supported Ubuntu distros a few weeks ago, but they're not on CRAN. For some reason not completely clear to me, t

[Bioc-devel] biocValid() and package version

Hi, I am using R-devel with R 3.5 as my package will be released with this version. I want to make sure that I am using the latest version of all packages: library("BiocInstaller") biocValid() Installed Built ReposVer airway "0.112.0" "3.4.3" "

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

On 05/10/2018 12:13 PM, Kenneth Condon wrote: Hi all, It sounds like the best thing to do is go back to the original binary and remove the source installation. Clarice, you know I can't even remember if I did that - I think I might try fix the current dependency issue tomorrow, but if any more

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

Hi all, It sounds like the best thing to do is go back to the original binary and remove the source installation. Clarice, you know I can't even remember if I did that - I think I might try fix the current dependency issue tomorrow, but if any more come up, Ill go back to the begining do as you s

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

Hi Kenneth, Given the link you're providing, it looks like you are looking for an R 3.5 package for Ubuntu Trusty (which is from 2014). Please see https://cran.r-project.org/bin/linux/ubuntu/ for the best place to ask this. Cheers, H. On 05/10/2018 10:20 AM, Kenneth Condon wrote: Hi all, I wa

Re: [Bioc-devel] CRAN R 3.5 binary - where is it?

Hi Kenneth, I see you're on Ubuntu 14.04. Have you tried in Terminal: sudo apt-get update sudo apt-get upgrade to upgrade your R version? Best, Clarice. Em qui, 10 de mai de 2018 às 14:20, Kenneth Condon escreveu: > Hi all, > > I want to submit a package to bioconductor this week but first I

[Bioc-devel] CRAN R 3.5 binary - where is it?

Hi all, I want to submit a package to bioconductor this week but first I want to build it on the latest R 3.5 release (with bioconductor 3.7). However, CRAN only has 3.4 binaries so I've had to build 3.5 from source which has unfortunat

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

I pushed a fix into R devel. On Wed, May 9, 2018 at 8:56 AM, Paul Shannon < paul.thurmond.shan...@gmail.com> wrote: > Hi Michael, > > Thank you for this work and the explanation. It’s good to know that my > problem will feed back into improvements in the methods package. > > I opted for a simple

Re: [Bioc-devel] BiocInstaller: next generation

On 05/10/2018 01:37 AM, Pariksheet Nanda wrote: Hi Henrik, On Thu, May 10, 2018 at 1:21 AM, Henrik Bengtsson < henrik.bengts...@gmail.com> wrote: May I suggest the package name: * Bioconductor The potential downside would be possible confusions between the version of this package versus t