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

[Martin Morgan]

On 03/16/2017 01:56 PM, Aayush Raman wrote:
> 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.

note that versions of packages added to Contributions/issues should be 
0.99.0, 0.99.1, 0.99.2, ....

Also, it is appropriate to ask questions specific to your package under 
the github issue associated with your package,

   https://github.com/Bioconductor/Contributions/issues/305

Martin

>
> 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
>>>
>>>         [[alternative HTML version deleted]]
>>>
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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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