Question: How to write the installation section in the vignette of a package that has not been sent into Bioconductor yet
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gravatar for k.patel5
8 weeks ago by
k.patel50
Newcastle University, UK
k.patel50 wrote:

Hello Bioconductor,

I am developing my first package as a part of my PhD and I am having some difficulties with understanding the procedures involved in correctly maintaining my package to the standard which the bioconductor new package guidelines state.

One of my areas of confusion is the requirement to show how to install my package from bioconductor on a vignette. The following line is found in the Package guidelines https://www.bioconductor.org/developers/package-guidelines/#vignettes.

"2. Add an “Installation” section that show to users how to download and load the package from Bioconductor."

I have not yet uploaded my package onto bioconductor (atm it is on a private github) so how could I add an installation for my package from bioconductor?

Do I just ignore the fact that my package is not on bioconductor yet, and proceed as shown below?

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Packagename")

Any help or guidance would be most appreciated, Krutik.

ADD COMMENTlink modified 8 weeks ago by shepherl ♦♦ 1.7k • written 8 weeks ago by k.patel50
Answer: How to write the installation section in the vignette of a package that has not
2
gravatar for shepherl
8 weeks ago by
shepherl ♦♦ 1.7k
United States
shepherl ♦♦ 1.7k wrote:

Yes you should ignore the fact that it is not on Bioconductor yet and include the above section. Keep in mind code like this, that shows installation, should be in a code chunk set with eval=FALSE so that it is not actually run (even when it is on officially on Bioconductor). If you are afraid you will have user find it you could add a temporary line that says pending acceptance .

ADD COMMENTlink written 8 weeks ago by shepherl ♦♦ 1.7k

This makes sense, thank you.

ADD REPLYlink written 8 weeks ago by k.patel50
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