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(inactive) Optimal p-value weighting with independent information (data and simulations) #396
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Hi @mshasan Thanks for submitting your package. We are taking a quick The DESCRIPTION file for this package is:
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I don't think this package is appropriate for Bioconductor. It seems from the Description like it is designed for 'reproducible research' rather than software that implements functions that are useful across different analyses. It doesn't have a vignette, which is a really central aspect of reproducible research and requirement for Bioconductor packages. The package contains functions that implement possibly useful calculations, but the interface to these functions is ad hoc and not amenable to reuse or interoperability across Bioconductor work flows. I also don't understand the relationship between this package and your earlier submission. Please elaborate. |
@mtmorgan Actually, when I was reading the instructions about linking webhook that was sent to me earlier, I found that I can add additional packages which are related to the previous package "OPWeight". That's why I added. I have not written the vignettes yet probably by this weekend I will be able to finish developing the vignettes. It was my misunderstanding. Regarding the relevance of this package to Bioconductor, there are four functions that are reusable and others are helpful if one wants to conduct simulations, especially using my method. In this packages, I essentially demonstrated how to apply the method I developed via simulations and data. I hope that will be more clear once I updated the vignettes. Thank you |
Why are the functions in this package not included in the earlier submission? |
Because in the previous package, I solely showed the method that I developed, but in the later one I showed a comparative study between several methods. For your convenience, I can referee two Bioconductor packages "IHW" and "IHWpaper". In the first, the author showed his method and in the second he showed comparative study results. My two packages would be similar. |
So it seems like the main problem here is that your package is missing the central piece -- the vignette? |
I closed this issue. Reopen it with a note to @mtmorgan when your package is complete. |
Please also make sure that has biocViews terms from the ExperimentData ontology. |
@mtmorgan package is now complete |
@mtmorgan I am wondering whether do I need to open a new issue for this package or will you update the existing issue? |
Your package has been approved for building. Your package is IMPORTANT: Please read the instructions for setting |
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". Please see the following build report for more details: http://bioconductor.org/spb_reports/OPWpaper_buildreport_20170613115736.html |
@lshep This package is an additional package depending on another package "OPWeight", which is currently under review by Bioconductor. That's why it is producing the error. |
@mshasan I am away on vacation this week but will review when I am back. Keep in mind, we will not accept this package until the dependent OPWeight is accepted, esp since we will not be able to have a full build report until OPWeight is available. In the meantime, as OPWeight gets reviewed, please apply any similar changes that may be suggested as far as coding standards and syntax in OPWeight to OPWpaper. I will provide a more detailed review of the package when I get back. |
Received a valid push; starting a build. Commits are: 7eb3bb8 Update DESCRIPTION |
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". Please see the following build report for more details: http://bioconductor.org/spb_reports/OPWpaper_buildreport_20170623060340.html |
Hi @mshasan,
When you've made the changes please bump the version to 0.99.2 and resubmit. Once these preliminary errors are cleaned up I'll do a full review. |
Received a valid push; starting a build. Commits are: 20ff93d version bumped |
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". Please see the following build report for more details: http://bioconductor.org/spb_reports/OPWpaper_buildreport_20170716173224.html |
@vobencha I addressed your comments and fixed the problems. I still have one problem related to the vignette. Would you be able to look at my vignette code, especially the first few lines where I used "load()" to load .RDATA. I tried many different ways but could not figure out the problems. My vignette code passed R CMD check but does not pass in the Bioconductor system. It seems that Bioconductor system is unable to load my saved data from the repository. |
I'll take a look at this tomorrow. |
Hi, I believe this is being submitted as a data package so we need to get it in the correct format. Data packages have a slightly different structure than software. Here are some examples that you can download and look at the source code: Please re-org the package so it has these directories and files:
Valerie |
fyi I'm out of the office July 26 - Aug 2. |
Checking in. Are you planning to submit a new version of this data package? |
@vobencha Thank you for the reminder. Yes, I will modify the package. I am currently writing my Ph.D. dissertation, therefore, struggling finding time. |
Should we close this issue and you can re-submit when you're ready? There is no rush to add the data package. |
Yes, you can close. I will reopen once I finish my dissertation defense.
Thank you
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