[Bioc-devel] Question about sumbition process and biocviews

Ioannis Vardaxis ioannis.vardaxis at math.ntnu.no
Sun Nov 6 22:54:37 CET 2016

Thanks for the answer,

I have some other questions about BiocCheck.

First I get the following warning:
* This is a software package, checking vignette directories...
    * ERROR: 'vignettes' directory!

I have my vignettes directory in the inst/doc/vignettes. If I change the
directory and place the vignettes in the top directory I don¹t get an
error from biocCheck, but I get a fatal error from Rcheck.

Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See

I read about unit tests, however the package is done and it works fine,
and at the same time I don¹t see how unit tests would benefit me based on
the functions in my package. Are them necessary?

Thirdly, I used the Rdpack for adding references to the roxynen files, but
I get an error from biocCheck that the macro is unknown. Is there another
way of using references in roxygen?

Finally, a question about coding: My longest function is 326 lines long,
and cannot be smaller, is that ok? I get a note in biocCheck. Moreover I
get the following note:
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 4 lines (0%) are > 80 characters
    * NOTE: Consider indenting lines with a multiple of 4 spaces; 462
      lines (6%) are not.

None of my code cross the 80 character line though and the spaces are
using the double tab that you need.

Ioannis Vardaxis

Stipendiat IMF

On 06/11/16 22:04, "Ioannis Vardaxis" <ioannis.vardaxis at math.ntnu.no>

>On 05/11/16 16:21, "Martin Morgan" <martin.morgan at roswellpark.org> wrote:
>>On 11/05/2016 11:12 AM, Ioannis Vardaxis wrote:
>>> Hi,
>>> When I upload my package to Github does the evaluation process start
>>>immediately? Or do I have to ask for it?
>>follow the instructions at
>>   https://github.com/Bioconductor/Contributions
>>when the issue is opened, someone (usually within 24 hours) moderates
>>your package so that the package is built and checked, and a reviewer
>>assigned. The reviewer will tackle your package without further
>>intervention from you and in due course, although many contributors end
>>up making substantial changes in response to the package builds before
>>the reviewer provides feedback.
>>> Furthermore, during the evaluation process do I get feedback about the
>>>dependencies of my package etc? I have those in my description file, but
>>>maybe they should be placed a little differently.
>>maybe, but if you have concerns then ask here first. No need to be
>>secretive about things, so don't hesitate to mention your package github
>>location (even before submission) and be specific and simple about your
>>> Moreover, when I run biocheck I get en error that I don't have any
>>>biocviews. I read the manual for creating those, but it is very
>>>difficult to understand. Do I do this after I upload the package to
>>>github or on my MAC?
>>Simply add a field biocViews: to the DESCRIPTION file, with terms chosen
>>from those available in the navigation widget at
>>   http://bioconductor.org/packages/devel/BiocViews.html#___Software
>>See for example the terms in
>>> Best
>>> --
>>> Ioannis Vardaxis
>>> Stipendiat IMF
>>> NTNU
>>> 	[[alternative HTML version deleted]]
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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