[Bioc-devel] Request to un-deprecate a package

Turaga, Nitesh Nite@h@Tur@g@ @ending from Ro@wellP@rk@org
Wed Dec 26 15:40:17 CET 2018


“biocLite" will stay deprecated for R version 3.5.2. Please note that the issue is not with “biocLite" but with “mmnet".

“mmnet” has been deprecated for R-3.5.z and is defunct for R-3.6.z.

There are other workaround solutions to this, where you may install the package from the tarball (https://www.bioconductor.org/packages/3.5/bioc/src/contrib/mmnet_1.13.0.tar.gz) using,

	R CMD INSTALL mmnet_1.13.0

This way, you can have the latest release version of R and have all packages up-to date except for “mmnet”.

But I think this question is better served answered in Bioc-devel. So I am forwarding the email. 



> On Dec 26, 2018, at 8:26 AM, osama ali <bioosama using aucegypt.edu> wrote:
> Dear Support Team
> Can I ask to have "biocLite" package not deprecated in R version 3.5.2 since I would like to use "mmnet" package in my metagenomic analysis in R by accessing my account in Mg-RAST server.
> I am not an experienced user but I get the following warning each time I call "biocLite()":
> "Warning messages:
> 1: 'biocLite' is deprecated.
> Use 'BiocManager::install' instead."
> I appreciate your kind support to solve this problem.
> Thank you very much
> Osama
> Osama S. Ali, MSc.
> Technical Operations Manager
> Biology Department, The American University in Cairo.
> AUC Avenue, P.O. Box 74
> New Cairo 11835, Egypt.
> tel.: 20.2.2615.2914
> fax: 20.2.2795.7565
> www.aucegypt.edu

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