[R-pkg-devel] Help with the warning : 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN

[Martin Morgan]

From Bioconductor's perspective, this warning is safe to ignore. But only CRAN knows whether they do or not.

Note the unusual situation that the check is on the 'devel' branch of R, but that the package that signals the warning comes from the branch of Bioconductor meant for R-3.5.* -- CRAN apparently uses 3.5.* package binaries (for both CRAN & Bioconductor) in R-devel.

Martin Morgan

On 3/6/19, 10:00 AM, "R-package-devel on behalf of Yonghui Dong" <r-package-devel-bounces using r-project.org on behalf of yonghui.dong using gmail.com> wrote:

    Dear all,
    
    I remember somebody has asked a similar question days ago, but the problem has not been solved. I am sorry that I ask this question again.
    
    My package can pass the CMD check in my local PC, while when I submit my package to CRAN, there is one warning:
    
    >Found the following significant warnings:
    Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
    
    One of my R package dependencies is a bioconductor package xcms. It seems that packages from Bioconducor cannot be installed now.
    
    More details are given in the directory:
    
    https://win-builder.r-project.org/incoming_pretest/Miso_0.2.1_20190304_095427/Windows/ <https://win-builder.r-project.org/incoming_pretest/Miso_0.2.1_20190304_095427/Windows/>
    
    Thanks a lot for your help.
    
    Dong
    	[[alternative HTML version deleted]]
    
    ______________________________________________
    R-package-devel using r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-package-devel