spatzie - Githubissues

kkrismer commented 3 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/jhammelman/spatzie

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bioc-issue-bot commented 3 years ago

Hi @kkrismer

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:

Type: Package
Package: spatzie
Title: Identification of enriched motif pairs from chromatin interaction
    data
Version: 0.99.0
Authors@R: 
    c(person(given = "Jennifer",
   family = "Hammelman",
   role = c("aut", "cre", "cph"),
   email = "jhammelm@mit.edu",
   comment = c(ORCID = "0000-0002-1008-2666")),
      person(given = "Konstantin",
   family = "Krismer",
   role = "aut",
   email = "krismer@mit.edu",
   comment = c(ORCID = "0000-0001-8994-3416")),
      person(given = "David",
   family = "Gifford",
   role = c("ths", "cph"),
   email = "gifford@mit.edu",
   comment = c(ORCID = "0000-0003-1709-4034")))
Description: Identifies motifs that are significantly co-enriched from
    enhancer-promoter interaction data. While enhancer-promoter annotation is
    commonly used to define groups of interaction anchors, spatzie also 
    supports co-enrichment analysis between preprocessed interaction anchors. 
    Supports BEDPE interaction data derived from genome-wide assays such as 
    HiC, ChIA-PET, and HiChIP. Can also be used to look for differentially 
    enriched motif pairs between two interaction experiments.
License: GPL-3
Depends: 
    R (>= 4.0)
Imports:
    BiocGenerics,
    biomaRt,
    BSgenome,
    GenomeInfoDb,
    GenomicFeatures,
    GenomicInteractions,
    GenomicRanges,
    ggplot2,
    IRanges,
    matrixStats,
    motifmatchr,
    S4Vectors,
    stats,
    SummarizedExperiment,
    TFBSTools,
    utils
Suggests:
    BiocManager,
    Biostrings,
    knitr,
    pheatmap,
    rmarkdown,
    testthat,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    TxDb.Mmusculus.UCSC.mm9.knownGene
VignetteBuilder: 
    knitr
biocViews: DNA3DStructure, GeneRegulation, PeakDetection, Epigenetics,
    FunctionalGenomics, Classification, HiC
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0a1cc8547891fc01b727610afac40dd2b2ced680

bioc-issue-bot commented 3 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 298396aa6c065e8cacdccb2999d3f66a72ef5342

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cfcbb04fd302c963571e8cad19a6e04753227f35

bioc-issue-bot commented 3 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: "WARNINGS, 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7a64108adbb8801ca850afbbaf660ca29fad8eb4

bioc-issue-bot commented 3 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. 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 78d9d225fc0e3dd4e58946ec7349975245191ee1

bioc-issue-bot commented 3 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.

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vjcitn commented 3 years ago

Thank you for this submission. The vignettes lack prose narration. Please write a paragraph of introduction and explanation of the key functions of your package.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3114a1640078d0badf573e98eb28ea0b2ad735c1

bioc-issue-bot commented 3 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.

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kkrismer commented 3 years ago

@vjcitn Thank you for your feedback and for keeping Bioconductor running!

I added an introduction explaining the objective of the analysis and the data involved, and explained the various steps and the key functions involved, for both vignettes.

vjcitn commented 3 years ago

Please look at these outputs of BiocCheck run on Bioc 3.14 in R 4.1 and rectify those you can. The LazyData prescription could be ignored if you use spatzie::[dataset] in code. I want to look further into that BiocCheck note.

[1] "'LazyData:' in the 'DESCRIPTION' should be set to false or removed"
[2] "Update R version dependency from 4.0 to 4.1."
[3] "Consider adding these automatically suggested biocViews: Transcription, CRISPR"
[4] " 'sessionInfo' not found in vignette(s)"
[5] "Recommended function length <= 50 lines."
[6] "Consider adding runnable examples to the following man pages which document exported objects:"
[7] "Usage of dontrun{} / donttest{} found in man page examples."
[8] "Use donttest{} instead of dontrun{}."
[9] "Consider shorter lines; 34 lines (2%) are > 80 characters long."
[10] "Consider multiples of 4 spaces for line indents, 318 lines(15%) are not."

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3ac321da6acb08cf7d776892c31ea3fa2010b1ab

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 85c5436146722fe3029394504a07a85d3e4df741

bioc-issue-bot commented 3 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c6d5c165c2c9aaf47fccd314a9f2c315ffccaae7

bioc-issue-bot commented 3 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, WARNINGS, 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 29c0bcd2f6a8b30070f13a4076372bb8d129e665

bioc-issue-bot commented 3 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ba0f8d2eb0685406522d4a706d30b0889997b33e

bioc-issue-bot commented 3 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a624d3679e23ef2e07e70372cba4eac001a34a70

bioc-issue-bot commented 3 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. 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kkrismer commented 3 years ago

[1] "'LazyData:' in the 'DESCRIPTION' should be set to false or removed"

I follow Hadley Wickham's recommendation (https://r-pkgs.org/data.html). Not sure what the philosophy behind that BiocCheck rule is, but since my data objects are only used in examples and unit tests, I figured it's better to load them lazily?

[2] "Update R version dependency from 4.0 to 4.1."

Done.

[3] "Consider adding these automatically suggested biocViews: Transcription, CRISPR"

I added 'Transcription'. 'CRISPR' is not a valid suggestion in this case.

[4] " 'sessionInfo' not found in vignette(s)"

Done.

[5] "Recommended function length <= 50 lines."

The 50 lines are exceeded in three cases and I'd argue refactoring these functions would not improve readability.

[6] "Consider adding runnable examples to the following man pages which document exported objects:"
[7] "Usage of dontrun{} / donttest{} found in man page examples."
[8] "Use donttest{} instead of dontrun{}."

I use dontrun in some examples to skip examples with long run times. I can't use donttest because of the newly introduced behavior of executing donttest blocks. I provide runnable examples wherever possible.

[9] "Consider shorter lines; 34 lines (2%) are > 80 characters long."

Reflowing these lines is either impossible (long package names) or undesirable (readability issues).

[10] "Consider multiples of 4 spaces for line indents, 318 lines(15%) are not."

These lines are aligned to function calls or definitions, i.e., the indentation is intentional.

Thanks again for your feedback!

About the errors/warnings from before, they were due to issues on the Bioconductor build server, thus unrelated to the code changes.

vjcitn commented 3 years ago

Thanks for the update. I still feel the vignette "single-call" could use some explanation. For example, the concluding heatmap suggests that YY1 motif coenrichment is stronger with AP2.1 than with YY1. Is this because you are using a "toy" motif database? Read the vignette like a user coming in cold and try to remedy basic puzzlement. I will look at the other vignette now.

vjcitn commented 3 years ago

Still pretty terse in the individual steps. Be sure any necessary references are available. For example, HOCOMOCO, and the spatzie paper, could be clearly referenced in the vignette to save reader the work of hunting around for them.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7cffc2e4ea116c6eefa0c47411d6c95df2d1f9a1

bioc-issue-bot commented 3 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kkrismer commented 3 years ago

@vjcitn

Thanks for your valuable feedback!

I've improved the vignettes by adding references to relevant papers, a link to the spatzie paper and website, additional explanations for individual steps, and a paragraph about the spatzie results, including a note that the motif database and the interactions data used in the vignette are only meant for demonstration purposes.

About the build error, these are again related to temporary issues on the Bioconductor build servers and not the code changes (there were none) - I suspect that the package cache on the build server is corrupt (e.g., package 'S4Vectors' required by 'GenomicRanges' could not be found).

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 706b6a2c574b1b8436b298f805ba92b707e12ebb

bioc-issue-bot commented 3 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. 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/spatzie to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

kkrismer commented 3 years ago

The only purpose of this last commit was to trigger a new build on the Bioconductor server to remove the wrong error label, see previous comment.

bioc-issue-bot commented 3 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

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vjcitn commented 3 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/kkrismer.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("spatzie"). The package 'landing page' will be created at

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spatzie #2123