curatedAdipoChIP: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)

MahShaaban 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/MahShaaban/curatedAdipoChIP

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bioc-issue-bot commented 5 years ago

Hi @MahShaaban

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: curatedAdipoChIP
Type: Package
Title: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes 
  (3T3-L1)
Version: 0.99.0
Year: 2019
Description: A curated dataset of publicly available ChIP-sequencing of 
  transcription factors, chromatin remodelers and histone modifications in the 
  3T3-L1 pre-adipocyte cell line. The package document the data collection,
  pre-processing and processing of the data. In addition to the documentation,
  the package contains the scripts that was used to generated the data.
License: GPL-3
Authors@R: person("Mahmoud", "Ahmed",
    email = "mahmoud.s.fahmy@students.kasralainy.edu.eg",
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-4377-6541"))
URL: https://github.com/MahShaaban/curatedAdipoChIP
BugReports: https://github.com/MahShaaban/curatedAdipoChIP/issues
Encoding: UTF-8
RoxygenNote: 6.1.1
Depends: R (>= 3.5),
    SummarizedExperiment
Suggests: 
    knitr,
    rmarkdown,
    GenomicFeatures,
    ChIPseeker,
    AnnotationDbi,
    S4Vectors,
    DESeq2,
    fastqcr,
    bib2df,
    devtools,
    testthat,
    readr,
    dplyr,
    tidyr,
    ggplot2
VignetteBuilder: knitr
biocViews: ExperimentData,
    GEO,
    ChIPSeqData,
    SequencingData

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, 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.

MahShaaban commented 5 years ago

Hi @lshep The build is failing because of an error in creating the vignette. The package contains an R object in data/ which is tracked using lfs. The system also generates an error because of a git tracked .gitattributes file. Is lfs allowed on the build system?

lshep commented 5 years ago

We do not support lfs; we encourage use of the Bioconductor Hubs (AnnotationHub/ExperimentHub) - Please see Creating ExperimentHub Package. Yes please remove .gitattributes from being git tracked with a git rm .

bioc-issue-bot commented 5 years ago

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

3595ce9 added vignette and news 2ba122a Merge branch 'master' of https://github.com/MahSha...

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:

9573a74 removed .rproj

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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

lshep commented 5 years ago

General

[ ] One of your package dependencoes bib2df has been removed from CRAN. Please remove this package dependency or reach out to CRAN/package maintainer to reinstate. We do not accept dependencies that are not on CRAN or Bioconductor. The SPB will not pick up on this change as it has already been installed before the package was removed from CRAN but as soon as we update to a newer version of R and flush the repo it will fail on all platforms.

https://cran.r-project.org/web/packages/bib2df/index.html

Build report

[ ] Please fix this note:
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ExperimentHub ExperimentHubData SummarizedExperiment These packages need to be imported from (in the NAMESPACE file)
[ ] We strongly encourage the use of unit tests. Unit tests can be a simple as checking to make sure the input/output data is of expected format and the like

NAMESPACE

[ ] As mentioned in build report above. Please import necessary packages that are listed in the depends of the Description.

vignette

[ ] Optional but I recommend renaming to package name or at least curatedchip.Rmd. It is much more intuitive for a user searching for a vignette to type vignette('curatedAdipoChIP') or vignette('curatedchip') rather than vignette('curatedchop_vignette')

Thank you and I look forward to accepting your package. Please address the above issues and when ready please comment here on the issue requesting a re-review.

bioc-issue-bot commented 5 years ago

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

5d3d9b7 import package deps

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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

MahShaaban commented 5 years ago

Thanks @lshep

I opened a new issue on the packages github repo. If the maintainer didn't reply soon I will look for a replacement for bib2df.
I imported the three packages, so this note should be fixed.
I was adivised by the reviewer in a previous submission of a similar packages to not use tests, here. I am also worried about the tests having to download and load the the data object every time they run.
I renamed the vignette file to curatedAdipoChIP.Rmd.

lshep commented 5 years ago

Ok. Let's wait and see what bib2df comes back with but otherwise I'm ready to accept.

lshep commented 5 years ago

Side note because we can still give them time to respond, Just keep me mind that the acceptance deadline is the 24th - so if you need time to make changes and make sure it checks ok just leave yourself a few days -

bioc-issue-bot commented 5 years ago

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

314d331 removed bib2df dep

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:

db0acb4 removed ExperimentHubData

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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

MahShaaban commented 5 years ago

I removed the bib2df dependency as I haven't got any reply on the issue. Please let me know if other changes are needed.

bioc-issue-bot commented 5 years ago

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!

mtmorgan commented 5 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/MahShaaban.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

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("curatedAdipoChIP"). The package 'landing page' will be created at

https://bioconductor.org/packages/curatedAdipoChIP

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.

Bioconductor / Contributions

curatedAdipoChIP: A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) #1059