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Bioconductor as a source for the dependencies of an R package?

Hello,

I am writing an R package and my dependencies are almost all bioconductor packages. It works on my computer because I already have all of them installed but it does skip them for being unavailable when loading my package. Anybody have a fix?

Thanks!

r bioconductor
• 8,144 views • link
updated by mramos148 • mramos148 • written by hakimelakhrass hakimelakhrass

Can you please explain a bit more?

Please make sure the following commands complete without ERROR or WARNING. This ERROR or WARNING most of the times solve lot of problem.

R CMD build [Package_name]
R CMD check [Package_name.tar.gz]
R CMD BiocCheck [Package_name.tar.gz]
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updated by Ram Ram • written by Tanvir Ahamed Tanvir Ahamed

Well I have the packages on my github and I load them through the devtools packages. In the Description I have my packages stated as such

Depends:
    R (>= 3.2.3),
    limma (<= 3.26.8),
    oligo (<= 1.34.2),
    pd.hugene.2.0.st (<= 3.14.1),
    genefilter (<= 1.52.1),
    annotate (<= 1.48.0),
    hugene20sttranscriptcluster.db(<= 8.4.0),
    affycoretools(<= 1.42.0)
License: GNU GENERAL PUBLIC LICENSE V3.0
LazyData: true
RoxygenNote: 5.0.1.9000

But I believe when you do that it looks for CRAN repo packages. I need it to get them from bioconductor.

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updated by Ram Ram • written by hakimelakhrass hakimelakhrass

Add a BiocViews entry to your package DESCRIPTION. Devtools will then detect your package as a Bioconductor package and add the proper Bioconductor repositories needed to install the dependencies.

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written by jimhester • jimhester

2 answers

The biocLite() function is the recommended way to access and install Bioconductor and Bioconductor-related packages. Take a look at the siteRepos argument to add the repository for your package and biocLite() will do the rest.

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updated by Ram Ram • written by Sean Davis Sean Davis

Ah yes I know how to install the packages for my own use. As you can see above I am writing a package that uses bioconductor packages. Are you saying I should instruct people who use my package to install it using biocLite() and then add my repo to that function?

Thanks!

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updated by Ram Ram • written by hakimelakhrass hakimelakhrass

Instruct them how to install biocLite() and then give them a command-line to install your package. It will look something like:

source('http://bioconductor.org/biocLite.R')
biocLite('MySuperSoftwareWithBioc',siteRepos=YOURREPOSITORY)
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updated by Ram Ram • written by Sean Davis Sean Davis

Dear Sean

I have a similar issue, and when I try to install my package using biocLite() it threw this error 

Error: Line starting '<!DOCTYPE html> ...' is malformed!

for comparison I also tried installing Gviz from bioconductor github mirror. Got the same error.

biocLite("Gviz", siteRepos = "https://github.com/Bioconductor-mirror/Gviz")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2 (2015-08-14).

Installing package(s) ‘Gviz’

Error: Line starting '<!.DOCTYPE html>...' is malformed!

What would be the solution to that?

Thanks, Vivek

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written by vivekbhr vivekbhr

Well, in order to use biocLite(), a formal R repository must be in place. The biocLite() approach will not work directly from github. Yes, I agree that this is less than ideal....

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written by Sean Davis Sean Davis

I see.. So how are the bioconductor developers working with github dealing with this situation (or are there any)? I think it would be helpful to either add github url support to biocLite(), or get the devtools::install_github to support bioconductor urls, whichever is easier ..

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written by vivekbhr vivekbhr

UPDATE : after @jimhester 's reply to the post I found that devtools already supports bioconductor packages while installing. I just had to populate biocViews in my package DESCRIPTION. So that install_github can pick up from that.

Apparantly biocLite would also work after this, if you use it like this: biocLite("Bioconductor-mirror/Gviz")

I guess this solves the issue.

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written by vivekbhr vivekbhr

biocLite("your/amazing") works too (via devtools), without requiring you to label your package with the biocViews term. It does this by setting the argument repos to a value that includes Bioconductor repositories, BiocInstaller::biocinstallRepos(), so you can do that, too install_github("your/amazing", repos=BiocInstaller::biocinstallRepos())

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written by Martin Morgan Martin Morgan

Could you please specify how you changed DESCRIPTION? I add a line "biocViews:", but installation of bioconductor packages still failed...

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written by Vivian • Vivian

@Vivian you need to add a term to biocViews. Eg :

biocViews : rnaseq

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written by vivekbhr vivekbhr

Update: This is not the recommended way of installing packages. Please use BiocManager::install("username/pkgrepo") to install a package from GitHub. We strongly recommend that you only do this in the devel version of Bioconductor (for developers); otherwise, simply install the package from either Bioconductor or CRAN using BiocManager::install("package").

• 0 views • link
written by mramos148 • mramos148

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