dvantwisk commented 4 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/Bioconductor/HMMRATAC

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

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[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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bioc-issue-bot commented 4 years ago

Hi @dvantwisk

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: HMMRATAC
Title: HMMRATAC - a semi-supervised machine learning approach for identifying
    open chromatin regions from ATAC-Seq data using Hidden Markov Models
Description: Hidden Markov ModeleR for ATAC-seq (HMMRATAC) is a semi-supervised
    machine learning appraoch for identifying open chromatin regions from
    ATAC-seq data. The ATAC-seq data is decomposed into different layers of
    coverage signal corresponding to the sequnced DNA fragments originated from
    nucleosomal regions. The relationship between the layers of signals at open
    chromatin. This package is an R implementation of the original java package
    meant to function within Bioconductor.
Version: 0.99.0
Encoding: UTF-8
VignetteBuilder: knitr
Author: Tao Liu, Daniel Van Twisk
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
    GenomeAnnotation
Depends: R (>= 3.5.0),
         rJava
Imports: rtracklayer
License: Artistic-2.0
RoxygenNote: 6.1.1
Suggests:
    ATACseqQC,
    BiocStyle,
    ChIPseeker,
    DiffBind,
    Gviz,
    HMMRATACData,
    JASPAR2018,
    Rsamtools,
    TFBSTools,
    knitr,
    rGREAT,
    testthat

bioc-issue-bot commented 4 years ago

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

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 4 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/HMMRATAC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

dvantwisk commented 4 years ago

AdditionalPackage: https://github.com/Bioconductor/HMMRATACData

bioc-issue-bot commented 4 years ago

Hi @dvantwisk, Thanks for submitting your additional package: https://github.com/Bioconductor/HMMRATACData. We are taking a quick look at it and you will hear back from us soon.

bioc-issue-bot commented 4 years ago

    **IMPORTANT**: Please read [this documentation][1] for setting
    up remotes to push to git.bioconductor.org. It is required to push a
    version bump to git.bioconductor.org to trigger a new build.

    [1]: https://bioconductor.org/developers/how-to/git/new-package-workflow/
    [2]: https://github.com/Bioconductor/Contributions#what-to-expect

bioc-issue-bot commented 4 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: "ABNORMAL". 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/HMMRATACData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mtmorgan commented 4 years ago

The version number of HMMRATACData should be 0.99.0. I'll update it.

bioc-issue-bot commented 4 years ago

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

17973fd Version bump to 0.99.0

mtmorgan commented 4 years ago

The package contains a file larger than 5MB, and these cannot be added to our git; should the be an ExperimentHub package?

  /data/65283_treat_rep1.chr22.20to30MB.bam

bioc-issue-bot commented 4 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/HMMRATACData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

nturaga commented 4 years ago

HMMRATAC and HMMRATACData

Build

ok

INSTALL

ok

DESCRIPTION

Use Authors@R instead of Author and Maintainer field.
Malformed Description field: should contain one or more complete sentences.

NAMESPACE

ok

R

WARNING: Update R version dependency from 3.5.0 to 4.0.
ok, seems like a wrapper function around a java based tool. Looks good.
jar file for HMMRATAC is in inst/ folder. This is ok.

man

The HMMRATACData package seems to need more work to populate the man pages and vignette.

* checking for missing documentation entries ... WARNING
Undocumented data sets:
  HMMRATACData

tests

There are no tests.

vignette

All the code chunks are set to eval = FALSE. The vignette is non-functional.

HMMRATACdata

Important details are missing, there is no vignette, R script or man pages. Please check

https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html

nturaga commented 4 years ago

Hi @dvantwisk ,

Since the package has been idle without any updates for about 30 days. I'm temporarily closing it. If you are able to get it into the next release, we can always reopen the package when you have time to address the issues in the review.

They are fairly minor, so take a look at them if you get a chance.

Hope things are going well.

Nitesh

bioc-issue-bot commented 3 years ago

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.

Bioconductor / Contributions

(inactive) HMMRATAC #1570

HMMRATAC and HMMRATACData

Build

INSTALL

DESCRIPTION

NAMESPACE

R

man

tests

vignette

HMMRATACdata