[Bioc-devel] question regarding man pages

Hello, We are working on our first Bioconductor package and have a question regarding man pages for helper functions We have several .R files which are all helper functions. 1) I am using RStudio for package development, and it creates .Rd files for all my .R files including helper files. Do

[Bioc-devel] need advice on how to fix build error in windows

Dear Biconductor team, We are developers of newly accepted Bioconductor package CINdex. Our package is meant for DNA copy number data analysis, and the example data we use is from Affymetrix SNP 6.0 , so we use 'pd.genomewidesnp.6' annotation package for Affymetrix SNP 6.0 in our vignette. Our

Re: [Bioc-devel] question regarding man pages

PACE >> file. R CMD check will clearly warn about missing documentation. I don't >> know how to deal with this in Rstudio. >> >> Best, >> Kasper >> >> >> On Tue, Mar 1, 2016 at 5:44 PM, Krithika Bhuvaneshwar >> <kb...@georgetown.edu>

[Bioc-devel] Vignette name not appearing on bioconductor package page

Hello, We are working on fine tuning our newly pre-accepted BioC package. We have two vignettes - an .Rnw file and another .Rmd file. If you see the screen shot in this email, you will see that there is no title or tag for my .Rnw file seen (first document in screen shot). But the .Rmd file

[Bioc-devel] need some advice for author listing on DESCRIPTION page

Hello, We are working on fine tuning how the citation should look in our DESCRIPTION of our pre-accepted package. We would like our R citation to appear like this: Author1, Author2, Author3, Author4, Author5, Author6 and Author7 (2016), PackageName. R package version 0.99.9. Just like how we

[Bioc-devel] SVN credentials

Hello We are authors of the newly accepted CINdex package. We have not received our SVN credentials yet. I believe today is the last day to make changes to the package before the new release . Also our package build was error free two days ago. Yesterday there was a build error only in windows

Re: [Bioc-devel] SVN credentials

Yes, that would be great. I will be the one making the updates. Thank you. -Krithika On Apr 2, 2016 10:45 AM, "Martin Morgan" <martin.mor...@roswellpark.org> wrote: > > > > On 04/02/2016 08:01 AM, Krithika Bhuvaneshwar wrote: >> >> Hello >> We ar

[Bioc-devel] Looking for small RNA-seq fastq files - to use in Rmarkdown

Dear Bioconductor community, I'm exploring options to create a Bioconductor or package related to RNA-seq data. Specifically, I am looking for an example RNA-seq dataset (fastq files, human genome, preferably liver cancer) to use in Rmarkdown files. As you know the input files to be used in

[Bioc-devel] our package build error in windows

Hello, It looks like our package CINdex has a build error in Windows (other OS are fine). http://bioconductor.org/checkResults/release/bioc-LATEST/CINdex/moscato2-buildsrc.html Seems to be problem with the "Xvector" package not present ? ** preparing package for lazy loading*Error in

[Bioc-devel] question regarding timeout

Hello, We are the maintainers of the CINdex package. I believe when the upgrade to the new Bioconductor version happened, the package times out in Windows environment during build. https://bioconductor.org/packages/release/bioc/html/CINdex.html Could you please let us know if we need to do

[Bioc-devel] CINdex package build error in Linux

Hello Bioconductor team, We are the creator and maintainers of the CINdex Bioconductor package. Last few days, we are seeing build errors in our package (See below). The package builds fine in Mac OS, but is giving the following error on Ubuntu OS.

[Bioc-devel] Question reg devtools in MacOS High Sierra

Hello, We are the package maintainers of the CINdex package. Our package is giving build errors and we are investigating why. I'm currently working on setting up the environment so I can replicate the error. I have a MacOS High Sierra. Here is what I did: * downloaded R 4.1 from

[Bioc-devel] Encountering Issues with Github sync

Hello, We are the package maintaines for the CINdex package. We have made changes in our package to address the build errors for the upcoming release. The latest code is here in our Gtithub account *https://github.com/ICBI/CINdex . *I'm trying to sync it with

Re: [Bioc-devel] Encountering Issues with Github sync

t; > git remote remove upstream > git remote add upstream g...@git.bioconductor.org:packages/CINdex.git > > On 2/25/21, 11:40 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" < > bioc-devel-boun...@r-project.org on behalf of kb...@georgetown.edu> wrote

Re: [Bioc-devel] Question reg devtools in MacOS High Sierra

ut why devtools or gert didn’t work. > > Best, > > > > On 2/11/21, 12:00 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" < > bioc-devel-boun...@r-project.org on behalf of kb...@georgetown.edu> wrote: > > Hello, > > We are the package mainta

Re: [Bioc-devel] Question reg devtools in MacOS High Sierra

not available for binary installation, > so you have to have additional system dependencies like libgit2 and openssl > also installed. > > Martin > > > On 2/11/21, 6:06 PM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" < > bioc-devel-boun...@r-pr

[Bioc-devel] Error in NSBS

Hello, I am working on creating a package, and have come across an issue. I have some R code in the "R" folder that works just fine when I test it. The code contains a function accepts a GRangesList as input. I call the function from my Rmarkdown file in the "vignette" folder. When I test the