[Bioc-devel] Question on the build and biocheck of the package

Hervé Pagès hpages at fredhutch.org
Thu Mar 16 17:57:35 CET 2017

Hi Ar,

On 03/15/2017 12:57 AM, Aayush Raman wrote:
> Hello Everyone,
> I have developed a Bioconductor package and submit the issue to build and
> check. I have some questions regarding on the build and BioCheck of the
> package. Here are the questions:
> 1. It has passed the build and check on Mac OS and Windows. However, when I
> am checking it on linux, I am getting the following error:
> "ERROR: dependencies ‘NMF’, ‘cvxclustr’ are not available for package
> ‘DASC’"
> Although, I know the NMF and cvxclustr are not present in the linux
> machine, I would like to know if it possible to build the package by
> installing other packages that my package depends on ? I am already
> mentioned it on DESCRIPTION file. Do I need to do anything else before
> submitting my package ?

You have these packages listed in your Imports field so they will be
automatically installed by the Single Package Builder on the 3 build
machines if they are not already present.

> 2. After successfully building (using R CMD build) and checking (R CMD
> check), I did a BiocCheck on my package. I got 2 warnings:
> a. WARNING: Use FALSE instead of F (found in 1 files)
> I am using a function called norm (from base package) where I need to
> specify the type. The type I would like to use is Frobenius norm which is
> specified by "F/f". How can I remove this warning ? or infom bioconductor
> about this warning prior to their checks ?

I don't see this when I run Rbiocdev CMD BiocCheck DASC_0.1.1.tar.gz.
Have you addressed this already? Please note that the way to specify
the type in base::norm() is with a 1-letter *string* ("O", "I", "F",
"M", or "2"). This has nothing to do with the use of F (unquoted) for
specifying the single logical value FALSE.

> b. WARNING: Add non-empty \value sections to the following man pages:
> data.Rd:
> data.Rd is a dataset that I will be uploading with our package. I would
> like to know how can I remove this error ?

Man pages for data sets need a \format section instead of a \value
section. If you have one, and R CMD BiocCheck still complains about
the lack of a \value section, please ignore the warning.

Hope this helps,


> Any help or advice would be much appreciated.
> Thanks,
> -Ar
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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