Re: [Bioc-devel] Vignette examples

2020-09-10 Thread Sean Davis
Hi, Emilie. A useful tidbit to include when asking questions such as yours is to include a link to the repository with code that folks can quickly go through. Is your code available? Sean On Thu, Sep 10, 2020 at 10:38 AM Emilie Secherre wrote: > Hello, > > > > I'm currently making a

Re: [Bioc-devel] FW: Java version issue on Bioconductor test platform

2020-09-10 Thread Pages, Herve
Hi Arman, Sure, if xlsx is broken and won't be fixed, use something else. Maybe try openxlsx? Similar to xlsx but doesn't require Java: https://CRAN.R-project.org/package=openxlsx But why would you use something else on Mac only? It's easier from a maintenance point of view if you use the

Re: [Bioc-devel] Vignette examples

2020-09-10 Thread Shepherd, Lori
Did you export the function in the package? Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Emilie

Re: [Bioc-devel] Vignette examples

2020-09-10 Thread Manders-2, F.M.
Hi Emilie, There are two possible problems I could think of. Did you remember to load your package in the vignette? Are your functions exported in the NAMESPACE of your package? With kind regards, Freek Manders On 10/09/2020, 16:38, "Bioc-devel on behalf of Emilie Secherre" wrote:

[Bioc-devel] Vignette examples

2020-09-10 Thread Emilie Secherre
Hello, I'm currently making a bioconductor package. When i'm running R CMD check, all the examples i used in function vignettes have one issue : could not find function "mypckgfunction". Is there a way to fix this issue ? The examples work perfectly when i'm using them in a R script, and are

Re: [Bioc-devel] fetch upstream of an existing package

2020-09-10 Thread Turaga, Nitesh
Please follow http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ . Notice that the branch name is RELEASE_3_11 (case sensitive). Nitesh From: Irene Zeng Date: Thursday, September 10, 2020 at 5:33 AM To: "Turaga, Nitesh" , "Shepherd, Lori" Cc: bioc-devel Subject: