pwrEWAS - Githubissues

stefangraw commented 5 years ago

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

Repository: https://github.com/stefangraw/pwrEWAS

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

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bioc-issue-bot commented 5 years ago

Hi @stefangraw

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: pwrEWAS
Title: A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS) 
Version: 0.99.0
Description: pwrEWAS is a user-friendly tool to assists researchers in the design and planning of EWAS to help circumvent under- and overpowered studies.
Author: Stefan Graw
Maintainer: Stefan Graw <sgraw@kumc.edu>
License: Artistic-2.0
LazyData: true
Imports:
    doParallel,
    abind,
    truncnorm,
    CpGassoc,
    shiny,
    ggplot2,
    parallel,
    shinyWidgets,
    BiocManager,
    doSNOW,
    limma,
    genefilter
Depends: 
    shinyBS,
    foreach
Suggests:
    knitr,
    rmarkdown
biocViews: DNAMethylation, Microarray, DifferentialMethylation
Encoding: UTF-8
RoxygenNote: 6.1.1
VignetteBuilder: knitr

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bioc-issue-bot commented 5 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

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 commented 5 years ago

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, TIMEOUT, 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.

stefangraw commented 5 years ago

So I have addressed the issue, but I am struggling to push the updated github repository to bioconductor. I have created the webhook. Is there anything else I need to do?

Thanks, Stefan

bioc-issue-bot commented 5 years ago

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

ae1cbd1 Update DESCRIPTION

stefangraw commented 5 years ago

Oh, just I missed the part where I need to increase the version number to trigger it.

AdditionalPackage: https://github.com/stefangraw/pwrEWAS_data

bioc-issue-bot commented 5 years ago

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 commented 5 years ago

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

41667b2 0.99.2

bioc-issue-bot commented 5 years ago

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 build report for more details.

bioc-issue-bot commented 5 years ago

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

f84b7d8 0.99.3

bioc-issue-bot commented 5 years ago

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 build report for more details.

bioc-issue-bot commented 5 years ago

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

a563fa7 0.99.4 Example #cores 4 -> 2

bioc-issue-bot commented 5 years ago

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.

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bioc-issue-bot commented 5 years ago

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

f3b6656 0.99.5 Handle NULL in combine function

bioc-issue-bot commented 5 years ago

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.

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bioc-issue-bot commented 5 years ago

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

cabdeed 0.99.6 invalid 'each' argument

bioc-issue-bot commented 5 years ago

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.

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bioc-issue-bot commented 5 years ago

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

40a316c 0.99.7 example had wrong vale: NcntPer = 10

stefangraw commented 5 years ago

There was a valid push, that was started to be built about 17 hours ago. But I have not received any results. Does that mean I was built without an error, or does is commonly take this long?

bioc-issue-bot commented 5 years ago

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

9bd955e 0.99.8 Identically to 0.99.7, but trying to trigg...

bioc-issue-bot commented 5 years ago

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

aed709d 0.99.9 Moved pop-up windows of drop down menus ab...

lshep commented 5 years ago

There was an issue with the Single Package Builder - I will manually kick off a build of your package but it should behave as normal and build upon the version bumps now.

bioc-issue-bot commented 5 years ago

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: "TIMEOUT". 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.

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bioc-issue-bot commented 5 years ago

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

03035fa 0.99.10 Reduced example

bioc-issue-bot commented 5 years ago

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.

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bioc-issue-bot commented 5 years ago

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

c466da6 0.99.11 Fix error in plot function example

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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

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bioc-issue-bot commented 5 years ago

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

01c6152 0.99.12 Further reduced examples

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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On one or more platforms, the build results were: "TIMEOUT". 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.

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bioc-issue-bot commented 5 years ago

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

4a922bd 0.99.13 Modified examples due to timeouts

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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bioc-issue-bot commented 5 years ago

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

57ef534 0.99.14 Commenting out examples for plot function...

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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bioc-issue-bot commented 5 years ago

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

cd953ec 0.99.15 Removed shiny example, because it require...

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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bioc-issue-bot commented 5 years ago

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

e1e0617 0.99.16 including examples for plot functions aga...

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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

8c23c4d 0.99.17 Subscribed to Bioc-devel email list

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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

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

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bioc-issue-bot commented 5 years ago

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

e73a352 0.99.18 Tigger bot again after subscription

bioc-issue-bot commented 5 years ago

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 build report for more details.

stefangraw commented 5 years ago

I am left with 2 error messages, that can not exactly be address:

* ERROR: Package Source tarball exceeds Bioconductor size
  requirement.
    Package Size: 104.0243 MB
    Size Requirement: 5.0000 MB

pwrEWAS depends on internal reference data, that is specific to tissue types. These reference data sets are critical for pwrEWAS and can not be excluded. I could make pwrEWAS download each reference data set from github (about 9mb) everytime needed, but this would make pwrEWAS not work without internet connection. Are there any other alternatives?

* ERROR: At least 80% of man pages documenting exported objects
  must have runnable examples. The following pages do not:
  pwrEWAS_shiny.Rd

pwrEWAS_shiny is initialtes a shiny user interface that requires user input and does not execute anything by itself and therefore will results in a timeout.

stefangraw commented 5 years ago

Dear @lshep or @hpages, Do you have any suggestions/recommendations how to address these issues?

Thanks, Stefan

lshep commented 5 years ago

@hpages will be primarily responsible for reviewing and making comments on this package but since he is currently on a short vacation: we do not allow software packages this large in Bioconductor. We would recommend providing the data in a separate experiment data package that accompanies the software package which would use ExperimentHub to cache the data.

stefangraw commented 5 years ago

@lshep , thank you for your recommendation. I will try to split the software and required data sets. Is there anything I can do about the runnable examples?

Thanks, Stefan

lshep commented 5 years ago

For now you can ignore the runnable examples and it can be addressed later on in the review process.

bioc-issue-bot commented 5 years ago

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

139930c 0.99.19 Outsourcing data

bioc-issue-bot commented 5 years ago

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 build report for more details.

bioc-issue-bot commented 5 years ago

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

5ee5630 0.99.20 download data from pwrEWAS_data

bioc-issue-bot commented 5 years ago

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 build report for more details.

Bioconductor / Contributions

pwrEWAS #1009