MOMA

[sunnyjones5]

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• Repository: https://github.com/califano-lab/MOMA

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[bioc-issue-bot]

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

c3f4bdf fixed re-add of BiocManager

[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 build report for more details.

[LiNk-NY]

Hi Sunny,

1. I thought I needed to import BiocManager to facilitate installation of it as a Bioconductor package and to have the install section in the vignette. Without having it imported I get a note/error about using it in the vignette so I'm not sure I can take it out or how to properly do so?

You should not run code to install packages in the vignette. Please add an eval = FALSE to the chunk options.

4. Unfortunately for certain/most results data structures the lists are too nested for them to be written by writeLines or to be easily tidied. From my searching on this sink was the best option. Is there a reason I shouldn't use it? I could add in a note/warning that alerts people that it's the function that's going to be used? Alternatively I could have them save as RData files or some other format that maintains their list structure? Another option would be to go back to not having the saveData function and allow users to use the data as they see fit as the main outputs are the plots generated by the makeSaturationPlots function? I can send over pictures/or longer descriptions of the results data if that would help explain why attempting to tidy them would be pretty difficult.

Not being able to easily tidy the data usually points to underlying data design issues. If possible, it may be better to add arguments for saveData that target specific pieces of the data structure.

5. Is the on.exit thing you mentioned related to the print options I currently change in the saveData() method?

Yes, the function shouldn't be changing the users' options.

Best, Marcel

[bioc-issue-bot]

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

ea440e5 change to saveData function and removing BiocManag...

[sunnyjones5]

Hi Marcel @LiNk-NY ,

As per your last comments I did the following:

1. Removed the BiocManager dependency and changed the eval to false in that part of the vignette so it runs without the install section.
2. Re-evaluated the "tidy-ability" of the results data and was able to convert most of the results data (7/9) to tables. I've changed the options for saving these to write.table in the saveData method. For the remaining 2, the results are lists that contain results of varying lengths/variables at multiple depths (see attached pictures) so I have just those 2 saving as rda's.

Let me know if that's okay! Is there anything else I need to address before the deadline on the 22nd?

Thanks, Sunny

(Clustering results run by testing PAM clustering with 2-15 centers. each result contains multiple pieces of information of varying sizes.)

(The genomic saturation information calculates the number/type of genomic events associated with each sample and with 1:100 regulators, saving the cumulative result with each addition regulator considered. Having them in a list like this is critical for internal downstream calculations. Honestly these are really intermediate results anyway as the summary of them is captured in the main plots made by makeSaturationPlots.)

[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 build report for more details.

[bioc-issue-bot]

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

8eb80bd pushing rebuild to bioconductor because of weird b...

[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 build report for more details.

[bioc-issue-bot]

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

7a1e0c4 re-pushing build to see if missing packages are th...

[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 build report for more details.

[LiNk-NY]

Hi Sunny, @sunnyjones5

Thank you for making those changes. They look great!

• The NEWS file should anticipate the release version 1.0.0.
• The name of the NEWS file should be NEWS.md otherwise it won't get picked up by BiocCheck. It currently is NEWS.Md. Use utils::news to check that the NEWS is correctly formatted.

Best, Marcel

[bioc-issue-bot]

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

32286ca removed old NEWS file e0639e1 added fixed NEWS file

[sunnyjones5]

Hi Marcel @LiNk-NY ,

This is great to hear!! I changed and pushed the version with the new NEWS.md file. Let me know what I need to do next to move it through to the next phase of submissions. Should I change the version number in the DESCRIPTION file now?

Thanks, Sunny

[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 build report for more details.

[sunnyjones5]

Hi Marcel @LiNk-NY and Lori @lshep ,

I just wanted to check to see if this package was confirmed to be in the next roll out of Bioconductor since this is the last day and it's still tagged as review in progress? Or if there is anything else I need to do?

Thanks, Sunny

[LiNk-NY]

Hi Sunny, @sunnyjones5

Thank you for sticking to it and making continual changes to your contribution. MOMA has been accepted. :tada:

Best regards, Marcel

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[sunnyjones5]

Amazing!! Thanks for your help! Best, Sunny

[mtmorgan]

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Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("MOMA"). The package 'landing page' will be created at

https://bioconductor.org/packages/MOMA

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.