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

Shepherd, Lori Lori.Shepherd at roswellpark.org
Thu Mar 16 19:30:55 CET 2017


1. Please ignore the dependency ERROR on tokay2 for now.  Some of this is on our end and we are in the process of correcting.

2. You have to make sure the webhook is set up for your package to automatically build on version bumps.  If you have not set up the webhook, please do so and then make another version bump in the DESCRIPTION file. See the instructions here:


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Aayush Raman <aayushraman09 at gmail.com>
Sent: Thursday, March 16, 2017 1:56:15 PM
To: Hervé Pagès
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Question on the build and biocheck of the package

Hello Hervé

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

1. This the report of the build of package from Bioconductor:
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.


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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