(inactive) Optimal p-value weighting with independent information (data and simulations)

[mshasan]

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

• Repository: AdditionalPackage: https://github.com/mshasan/OPWpaper

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[bioc-issue-bot]

Hi @mshasan

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: OPWpaper
Type: Package
Title: Reproduce figures and simulations of OPWeight
Version: 0.99.0
Date: 2017-04-18
Author: Mohamad S. Hasan
Maintainer: Mohamad S. Hasan <shakilmohamad7@gmail.com>
Description: To produce the figures and the simulations results, an extensive simulations
  has been conducted in the paper Hasan and Schliekelman (2017). In this
  package, we wraps the functions needed to reproduce the figures 
   and the simulations results described in the paper. We also showed 
   real life examples.
Depends: 
    R (>= 3.3.0),
    OPWeight
License: Artistic-2.0
LazyData: true
Imports:
    cowplot,
    ggplot2,
    IHW,
    mvnfast,
    qvalue,
    reshape2,
    stats,
    tibble
Suggests:
    BiocStyle,
    DESeq2,
    devtools,
    gridExtra,
    knitr,
    rmarkdown,
VignetteBuilder: knitr
biocViews:
    MultipleComparison,
    RNASeq
RoxygenNote: 6.0.1
URL: https://github.com/mshasan/OPWpapaer
Bugreports: https://github.com/mshasan/OPWpaper/issues

[mtmorgan]

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.

[mshasan]

@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

[mtmorgan]

Why are the functions in this package not included in the earlier submission?

[mshasan]

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.

[mtmorgan]

So it seems like the main problem here is that your package is missing the central piece -- the vignette?

[mtmorgan]

I closed this issue. Reopen it with a note to @mtmorgan when your package is complete.

[mtmorgan]

Please also make sure that has biocViews terms from the ExperimentData ontology.

[mshasan]

@mtmorgan package is now complete

[mshasan]

@mtmorgan I am wondering whether do I need to open a new issue for this package or will you update the existing issue?

[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/OPWpaper_buildreport_20170613115736.html

[mshasan]

@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.

[lshep]

@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.

[bioc-issue-bot]

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

7eb3bb8 Update DESCRIPTION

[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/OPWpaper_buildreport_20170623060340.html

[vobencha]

Hi @mshasan, We have reassigned both your data and software packages to me so one person can review both. For starters, please address these issues in the Single Package Builder output:

1) non-portable paths

* checking for portable file names ... NOTE
Found the following non-portable file paths:
  OPWpaper/vignettes/FWER_and_FDR_cache/html/fdr_ey_notequals_et2_9404802ef1bebe4fd4a29a160e5426f5.RData
  OPWpaper/vignettes/FWER_and_FDR_cache/html/fdr_ey_notequals_et_f14ecd09d311ed64884791527da9b689.RData
  OPWpaper/vignettes/FWER_and_FDR_cache/html/fwer_ey_notequals_et2_66785310a27dacda55b0b87bdf4b790d.RData
...

2) reduce example runtime

* checking examples ... [108s/111s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
probRel_filterVstest_effect 77.466  0.495  80.136
simu_fwer                   19.468  0.252  20.472

3) use TRUE and FALSE

* Checking for T...
    Found T in R/weight_byEffect_cont.R (line 79, column 46)
    * WARNING: Use TRUE instead of T (found in 1 files)
* Checking for F...
    Found F in vignettes/Power.Rmd
    * WARNING: Use FALSE instead of F (found in 1 files)

4) man pages need non-empty \value and run-able examples

* Checking man pages...
    * WARNING: Add non-empty \value sections to the following man
      pages: man/weightSum_by_c.Rd
* Checking exported objects have runnable examples...
    * ERROR: At least 80% of man pages documenting exported objects
      must have runnable examples. The following pages do not:
      nice_plots.Rd, prob_weight_plots.Rd, ranksProb_compare_plots.Rd,
  ranksProb_compare.Rd

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. Thanks. Valerie

[bioc-issue-bot]

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

20ff93d version bumped

[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/OPWpaper_buildreport_20170716173224.html

[mshasan]

@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.

[vobencha]

I'll take a look at this tomorrow. Valerie

[vobencha]

Hi, When you use load() the file type must be saved using save() and must be location in the data/ directory of the package.

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: http://www.bioconductor.org/packages/release/BiocViews.html#___ExperimentData

Please re-org the package so it has these directories and files: R/ tests/ man/ vignettes/ data/: All .rds files go here inst/extdata/: All non-.rds files go here external_data_store.txt: This file states where the data files are. For example, here is what the file looks like in the minfiData package:

~/minfiData >cat external_data_store.txt 
data
inst/extdata

Valerie

[vobencha]

fyi I'm out of the office July 26 - Aug 2. Valerie

[vobencha]

Checking in. Are you planning to submit a new version of this data package? Valerie

[mshasan]

@vobencha Thank you for the reminder. Yes, I will modify the package. I am currently writing my Ph.D. dissertation, therefore, struggling finding time.

[vobencha]

Should we close this issue and you can re-submit when you're ready? There is no rush to add the data package.

[mshasan]

Yes, you can close. I will reopen once I finish my dissertation defense. Thank you

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On Thu, Aug 24, 2017 at 9:40 AM, vobencha notifications@github.com wrote:

Should we close this issue and you can re-submit when you're ready? There is no rush to add the data package.

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