[Bioc-devel] external dependencies

Anna Gogleva gogleva.a.a at gmail.com
Mon Oct 2 15:40:43 CEST 2017

Dear Martin and Vincent,

Thanks for your feedback. Here is the current package repository:

I still need to run more tests on mac and clean the code a bit.
But probably this would be sufficient to say whether the package is
compatible with Bioconductor in principle or not.


On 2 October 2017 at 14:11, Vincent Carey <stvjc at channing.harvard.edu>

> I'd also comment that if you make the package visible I would be willing
> to have a look at the issues involved in porting to windows.  No guarantees
> but at least get some sense of context.
> On Mon, Oct 2, 2017 at 9:04 AM, Martin Morgan <
> martin.morgan at roswellpark.org> wrote:
>> I want to add, though, that OS-specific functionality and system
>> requirements greatly limit the utility of your package and, like the
>> OS-specific dependencies your package depends on, serves as a kind of virus
>> that makes any other package that uses yours also not operable on the
>> unsupported OS. You're also introducing complexity into the build system
>> and for potential users, and especially to your own package where you need
>> to effectively navigate around idiosyncrasies of the third-party software.
>> So while technically possible, I'd take a deep dark look at the soul of
>> your package and ask whether it is really necessary to do this. Maybe the
>> functionality offered by the system dependency is not core to what your
>> package offers, or an alternative cross-platform solution provides
>> something that is 'good enough', or the author of the upstream dependency
>> can be convinced to make their package more user friendly, or the specific
>> functionality provided by the OS-specific software can be spun off to an
>> independent R package.
>> I know that many Bioc developers are on linux or mac, but more than 1/2
>> of our web and support site visitors are on Windows, so you're losing 1/2
>> your audience and impact.
>> Martin
>> On 10/02/2017 08:40 AM, Anna Gogleva wrote:
>>> Dear Lori,
>>> Thanks a lot for the clarification.
>>> I will incorporate os checks in my unit tests and examples.
>>> Thanks,
>>> Anna
>>> On 2 October 2017 at 12:30, Shepherd, Lori <
>>> Lori.Shepherd at roswellpark.org>
>>> wrote:
>>> You can still submit to bioconductor despite this limitation.  You could
>>>> also do a os check in the examples and tests that fail on windows and
>>>> make
>>>> a comment that this is the case.  If the program is not meant to run in
>>>> windows there is options to handle that as well and the review assigned
>>>> to
>>>> you can assist you with this.  If you feel the package is otherwise
>>>> ready
>>>> to submit to Bioconductor for review I would proceed.
>>>> https://github.com/Bioconductor/Contributions
>>>> 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 Anna
>>>> Gogleva <gogleva.a.a at gmail.com>
>>>> *Sent:* Monday, October 2, 2017 5:36:57 AM
>>>> *To:* bioc-devel at r-project.org
>>>> *Subject:* [Bioc-devel] external dependencies
>>>> Dear Bioconductor Team,
>>>> I have written a package and was planning to submit it to Bioconductor
>>>> one
>>>> day. The package provides a set of wrapper functions around several
>>>> existing command line tools to construct scalable and reproducible
>>>> pipelines for secretome prediction.
>>>> The package requires several external system dependencies to be
>>>> installed
>>>> in order to work (listed in the SystemRequirements filed). I have a
>>>> top-level README describing in detail how to install the required
>>>> dependencies and a shell script to automate this process. The thing is,
>>>> some of the external dependencies were not designed to work on Windows -
>>>> causing certain unit tests and examples to fail during the automatic R
>>>> CMD
>>>> check on Windows.
>>>> I have run R CMD check on Mac and Linux and the package passes without
>>>> errors, warnings or notes. It also satisfies the remaining requirements
>>>> from the recommended package checklist.
>>>> What would be the best way to proceed? Would it be still ok to submit
>>>> the
>>>> package though it is not fully functional on Windows due to
>>>> unavailability
>>>> of certain external dependencies?
>>>> Thank you for your advice,
>>>> Anna Gogleva
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