Question

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

2

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8.2 years ago

hakimelakhrass ▴ 80

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 • 5.4k views

ADD COMMENT • link updated 11 months ago by mramos148 ▴ 30 • written 8.2 years ago by hakimelakhrass ▴ 80

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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]

ADD REPLY • link updated 5.6 years ago by Ram 43k • written 8.2 years ago by Tanvir Ahamed ▴ 350

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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.

ADD REPLY • link updated 5.6 years ago by Ram 43k • written 8.2 years ago by hakimelakhrass ▴ 80

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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.

ADD REPLY • link 8.1 years ago by jimhester ▴ 10

Ram · Answer 1 · 2016-02-22

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8.2 years ago

Sean Davis 26k

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.

ADD COMMENT • link updated 5.6 years ago by Ram 43k • written 8.2 years ago by Sean Davis 26k

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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!

ADD REPLY • link updated 5.6 years ago by Ram 43k • written 8.2 years ago by hakimelakhrass ▴ 80

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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)

ADD REPLY • link updated 5.6 years ago by Ram 43k • written 8.2 years ago by Sean Davis 26k

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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

ADD REPLY • link 8.1 years ago by vivekbhr ▴ 690

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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....

ADD REPLY • link 8.1 years ago by Sean Davis 26k

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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 ..

ADD REPLY • link 8.1 years ago by vivekbhr ▴ 690

score 0 · Answer 2 · 2016-03-14

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8.1 years ago

vivekbhr ▴ 690

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.

ADD COMMENT • link 8.1 years ago by vivekbhr ▴ 690

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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())

ADD REPLY • link 8.1 years ago by Martin Morgan ★ 1.6k

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

ADD REPLY • link 7.7 years ago by Vivian • 0

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

biocViews : rnaseq

ADD REPLY • link 7.7 years ago by vivekbhr ▴ 690

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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").

ADD REPLY • link 11 months ago by mramos148 ▴ 30