(inactive) NOMAD

[carlmurie]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/carlmurie/NOMAD

Confirm the following by editing each check box to '[x]'

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• [ x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

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[bioc-issue-bot]

Hi @carlmurie

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: NOMAD
Type: Package
Title: Normalization of Mass Spectrometry Data
Version: 0.99.0
Date: 2015-01-15
Author: Carl Murie
Maintainer: Carl Murie <cmurie@fredhutch.org>
Description: The NOMAD R package that implements an ANOVA normalization method designed for iTRAQ mass spectrometry data in a computationally efficient manner.
NeedsCompilation: no
Depends: 
    R (>= 3.3.3), 
    dplR, 
    stringr, 
    graphics, 
    stats
LazyLoad: true
License: GPL (>=2)
biocViews: Normalization, Proteomics, MassSpectrometry 
RoxygenNote: 6.0.1

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/NOMAD_buildreport_20170330173142.html

[mtmorgan]

@LiNk-NY will review this package, but it's surprising that it makes no use of other Bioconductor packages or best practices.

It seems like your data is frequently a data.frame (confusingly described as a \code{vector} and 'matrix' in the documentation) with specific columns. Rather than checking for this repeatedly, it makes much more sense to create an S4 class and validity method that ensures, in one place so guaranteeing consistency, that the data is correctly formatted.

A big part of Bioconductor is interoperability with other software packages with similar functionality. Often this is enhanced by using data representations defined in other packages. So maybe you don't need to re-invent a class, but instead can identify other packages that define similar representations and re-use them.

[LiNk-NY]

Hi @carlmurie, Any thoughts about moving forward with the comment above?

Regards, Marcel

[carlmurie]

Hi,

Yes, I could convert the data.frame to an S4 object. Maybe I misunderstood but I thought that a reviewer was going to look at the package and make recommendations. I was going to wait for that before I started modifying the code.

Carl

On Tue, Apr 4, 2017 at 9:43 AM, Marcel Ramos notifications@github.com wrote:

Hi @carlmurie https://github.com/carlmurie, Any thoughts about moving forward with the comment above?

Regards, Marcel

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/336#issuecomment-291560215, or mute the thread https://github.com/notifications/unsubscribe-auth/ABY1bov7asEtkvhmy_S8zYSaZJp9YfTnks5rsnNOgaJpZM4Mu8I2 .

[LiNk-NY]

Hi Carl, @carlmurie

Yes, you can use an S4 class to represent your data and include validity checks. You should also look at what is available in Bioconductor for this type of data and reuse existing software.

Interoperability is a major factor in our review process and we want to ensure that your package is working well with the Bioconductor infrastructure before the review process. Otherwise, we'd be reviewing all non-Bioconductor packages submitted. Thank you.

Regards, Marcel

[LiNk-NY]

Your issue has been closed due to inactivity. To submit your revised package to Bioconductor, please create another issue. Thank you. -Marcel