Re: [Bioc-devel] UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 234445: ordinal not in range(128)

2020-06-04 Thread Nitesh Turaga
Hi, Just to keep the mailing list informed. This has been solved. Please push again. Nitesh > On May 18, 2020, at 11:20 AM, Jakob Theorell > wrote: > > Dear all, > I guess this is related to some to me unknown failure on my side to avoid > merge conflicts, but I now get the above error when

Re: [Bioc-devel] SSH Issues

2020-06-04 Thread Nitesh Turaga
Hi Chris and Benjamin, I’m trying to set things in order so that access is resumed back to normal for the 7 packages It seems that there are multiple email address listed for Benjamin -- ‘benjamin.haibe.ka...@utoronto.ca’ and 'bhklab.resea...@gmail.com’. Can we default to only one email addr

Re: [Bioc-devel] Bioconductor package tidybulk

2020-06-04 Thread Shepherd, Lori
The master branch is the development branch (Bioc 3.12) . The version of x.y.z The y is always odd in devel and even in release. This is the very first section on the page you referenced. http://bioconductor.org/developers/how-to/version-numbering/ We do not jump full y versions in th

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-04 Thread Martin Morgan
None of the items below are \Sexp{}. Only \Sexp{} are \Sexp{}. I built your package from github git clone https://github.com/stemangiola/tidybulk R CMD build tidybulk R CMD BiocCheck tidybulk and saw many (easily fixable) problems, but I did not see a line You have initialised objec

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-04 Thread Lluís Revilla
Hi Stefano, About 1) you can document internal functions but remove them from the index if you use #' @keywords internal tag. See the vignette of roxygen2 https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html under Other tags. About 2) perhaps you have too many/long examples? Hope th

Re: [Bioc-devel] How I hide non-exported function from the manual

2020-06-04 Thread stefano
Thanks to Both, since I cannot find any exhaustive documentation about \Sexpr{} I will ask here. - is \examples{} an \Sexpr{} - is \value{} an \Sexpr{} - is \arguments{} an \Sexpr{} - is \item{} an \Sexpr{} Because although all my functions in the manual have, for example \value{}, non of t

Re: [Bioc-devel] git push permission denied

2020-06-04 Thread Christian Mertes
Dear Nitesh, thank you for resolving this so quickly! Best, Christian On Tue, 2020-06-02 at 11:53 -0400, Nitesh Turaga wrote: > Hi, > > This is because you don’t have access to FRASER package. Only Ines > Scheller seems to have access to it. > > I’ve made the change and you should have acces