Re: [Bioc-devel] question regarding man pages

Btw. a common (but not required) convention is that unexported helper functions start with . Personally I find that helpful. On Tue, Mar 1, 2016 at 8:20 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > You only need to document functions which are exported in the NAMESPACE >

Re: [Bioc-devel] question regarding man pages

You only need to document functions which are exported in the NAMESPACE 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 wrote: > Hello, >

[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] License question for experimental data package

Dear Bioc developers, I recently downloaded three publicly available single-cell RNA-seq datasets from the NCBI GEO/SRA repository and created an R package with some gene-level summaries (read counts and FPKMs). I'm currently using the package locally for my own tests, but I'm thinking that this

Re: [Bioc-devel] workflow builder "Failed to check repository revision..."

Thanks, there was a password change and some things had to be tweaked as a result. Should be building now: http://docbuilder.bioconductor.org:8080/job/rnaseqGene/6/label=master/console Dan - Original Message - > From: "Michael Love" > To: "bioc-devel"

[Bioc-devel] workflow builder "Failed to check repository revision..."

hi, I committed a new version of the rnaseqGene workflow about an hour ago and am waiting on the workflow builder to start running. There may be something going on here: Started on Mar 1, 2016 10:28:00 AM Received SCM poll call on master for rnaseqGene on Mar 1, 2016 10:28:01 AM ERROR: Failed

Re: [Bioc-devel] Noticed change of version for some packages in BioC 3.2

The main reason for packages to change in release is because of bug fixes, also documentation enhancements. You should not expect the versions in release to be frozen. Dan - Original Message - > From: "Bernd Klaus" > To: "Stefano Berri" ,

Re: [Bioc-devel] Noticed change of version for some packages in BioC 3.2

Hi Stefano, developers are not supposed to change the package fundamentally in the release branch, however small fixes are allowed to be back-ported and marked by a bump of the last digit: http://bioconductor.org/developers/how-to/version-numbering/ (E.g. fixing typos in the vignette or

[Bioc-devel] Package reference manuals in html

Dear all, I find the http://www.rdocumentation.org/ site very useful to refer to nicely formatted online man pages individually. Unfortunately, this resource is terribly outdated and not maintained anymore. I was wondering if Bioconductor had any interest in serving an html version of

[Bioc-devel] Noticed change of version for some packages in BioC 3.2

Hi. Maybe I am getting something wrong, but I am pretty sure I noticed the change of package version for some Bioconductor packages in 3.2 In particular - IRanges_2.4.6.tar.gz \ + IRanges_2.4.8.tar.gz \ - Biostrings_2.38.3.tar.gz \ + Biostrings_2.38.4.tar.gz \ -