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

[Aayush Raman]

Hello Hervé

Thanks for a quick reply. I have some more questions:

1. This the report of the build of package from Bioconductor:
http://bioconductor.org/spb_reports/DASC_buildreport_20170306051600.html.
Here, you will see *dependencies error* in the tokay2 BUILD SRC output.
Should I include these packages under Depends or Imports is fine ? Just to
make sure, my package uses NMF function from NMF package and another
function from cvxclustr package.

2. I have made some changes in my code (https://github.com/aayushraman/DASC)
and have changed the version to 0.1.1. I would like to know if I have to do
anything else to inform the Single Package Builder to rebuild and check my
package again.

Thanks,
-Ar


On Thu, Mar 16, 2017 at 11:57 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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,
>
> H.
>
>
>> Any help or advice would be much appreciated.
>>
>> Thanks,
>> -Ar
>>
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>>
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>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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