zFPKM

[ronammar]

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• Repository: https://github.com/ronammar/zFPKM

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[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

c53d03c Bugfix in documentation

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/zFPKM_buildreport_20170628155606.html

[ronammar]

Hi @LiNk-NY, thanks for your feedback. I've updated my repository to include SummarizedExperiment where appropriate. Please let me know if anything else is required after review.

[LiNk-NY]

Hi Ron, @ronammar Thanks for making that change.

Your package is most of the way there. There are some minor issues that can be addressed.

• Make use of helper functions to avoid repeating yourself in functions like zFPKMPlot and zFPKM.
• Separate functionality. PlotGaussianFit should be two different functions the gaussian fit function and the plotting function. Please separate the two. This will avoid calling a plotting function when you just want to fit the model as in zFPKMTransform.

Please consider that most plotting functions output to the device and not to a file. A user wishing to save a file will do so in the format of their choosing. You should just limit the plotting function to returning the figure in the graphics device.

Regards, Marcel

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

ccd387a Refactor to satisfy Bioconductor style suggestions

[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: "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/zFPKM_buildreport_20170710112248.html

[ronammar]

Hi Marcel (@LiNk-NY),

Thanks again for your review and the suggestions to improve the package.

Note, the recent build report appears to have an error and was run on a single OS. I'm uncertain as to the cause- Is this an error on my end?

Addressing your feedback:

• I am now using a helper function and have removed redundant calls.
• The PlotGaussianFitDF function performs plotting-specific scaled fits that are distinct from the zFPKM transformation, but are required for the final plot. This computation is easier to understand within the context of the PlotGaussianFitDF function rather than separated. So, the zFPKMTransform and plotting fitting are independent and distinct, even though they appear similar.

Thanks! Ron

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/zFPKM_buildreport_20170710114926.html

[LiNk-NY]

Hi Ron, @ronammar Thanks for looking into it.

• Please keep a NEWS file in the inst folder in your package for updates on the versions.
• If your imports are not central to what your package does, then they should be in suggests. It seems to me like checkmate can be an optional package dependency and is not needed.

Minor

• check class membership with is(object, "SummarizedExperiment")
• Use the more robust double bracket extractor method rather than the $ (e.g., d[["m"]] vs d$m)
• avoid using "this" as object names, it's not descriptive

The package is close to being accepted. Thanks. Regards, Marcel

[LiNk-NY]

Hi Ron, @ronammar The package is close to completion and should be accepted as soon as you make those minor changes. Are you able to make those changes and bump the version?

Thanks, Marcel

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

7c7f253 Updated with major and minor changes

[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: "WARNINGS". 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/zFPKM_buildreport_20170727234329.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

8be4b50 Fixing warning from auto-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: "WARNINGS". 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/zFPKM_buildreport_20170728000000.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

11f2db6 Updated zFPKM documentation

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/zFPKM_buildreport_20170728000956.html

[ronammar]

Hi Marcel (@LiNk-NY),

Thanks again for your review and the suggestions to improve the package. I have updated the package accordingly. Please advise.

Regards, Ron

[LiNk-NY]

Thanks Ron @ronammar for making those changes. Thank you for submitting to Bioconductor. Your package has been accepted.

Best regards, Marcel

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor svn repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!

[ronammar]

Excellent! Thanks, Marcel @LiNk-NY!

[ronammar]

Hello @mtmorgan @LiNk-NY, I've added a requested biocViews tag and pushed. How do I trigger a new build? Thanks!

[mtmorgan]

Since your package has been accepted, changes need to be made to the Bioconductor git repository rather than to your github repository. Resources are available at http://bioconductor.org/developers/how-to/git/ ; be sure to use the bioc-devel mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel for communication about issues like this.