Submitting Package WhistleR

ZW-xjtlu 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/ZW-xjtlu/WhistleR

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bioc-issue-bot commented 3 years ago

Hi @ZW-xjtlu

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: WhistleR
Type: Package
Title: Comprehensive Annotation of Predictive Features for Range-based Genomic Data
Version: 0.99.0
Author: Zhen Wei
Maintainer: Zhen Wei <zhen.wei10@icloud.com>
Description: Extract predictive genomic features using the interaction between genomic properties and genomic regions. WhistleR aims to facilitate feature engineering for the predictive modeling of genomic assays. The package can enumerate a large number of genome-derived features through the combination between genomic properties (e.g., region length, region topologies, region sequence content, region clustering effects, region scores) and genomic regions (e.g., exons, introns, promoters, 5'UTR, CDS, 3'UTR, transcripts, genes). Compared with only using sequence features, adding the comprehensive features of region properties can enhance the performance of predictive modeling. In addition, the region property features are highly interpretable via the regression analysis and the machine learning interpretation techniques, which can facilitate the identification of key factors affecting the targeted genomic quantities.
License: LGPL (>= 3)
Imports: BiocGenerics, Biostrings, GenomeInfoDb, GenomicRanges, GenomicScores, BSgenome, IRanges, ensembldb, matrixStats, methods, GenomicFeatures, gtools, stats, S4Vectors, utils
Depends: R (>= 4.0)
Suggests: knitr, rmarkdown, ggplot2, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.0
biocViews: FunctionalPrediction, FeatureExtraction, GenomeAnnotation, FunctionalGenomics,
        Classification, Clustering, Regression
NeedsCompilation: no

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/WhistleR 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: 9143be39359dc39e5a3230fd1dafcb28c88e59f5

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/WhistleR 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: 715a310b7f6b393ef00489a1438d274c84e21587

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/WhistleR 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: 717be43e68676904133bc20f44887e1ccf19ca06

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/WhistleR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

hpages commented 3 years ago

Thanks for the submission. Package looks good.

2 minor things:

(1) The vignette says:

WhistleR can be installed from both bioconductor and github.

Please note that we strongly discourage installing Bioconductor packages from GitHub. Because of Bioconductor 6-month release cycles and because Bioconductor has a notion of release and devel, Bioconductor users should always use BiocManager::install() to install packages. This will spare them a lot of headaches with version mismatches. Please instruct your users to install the package with BiocManager::install() and do not encourage them to install from GitHub.

(2) You can do:

X <- makeGRangesFromDataFrame(X_df)

instead of:

X <- GRanges(seqnames = X_df[,1],
ranges = IRanges(start = X_df[,2],
end = X_df[,3]),
strand = X_df[,5])

Thanks, H.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 28a7c85774136504e319edd02c37e21d5514bdca

ZW-xjtlu commented 3 years ago

Thanks for the submission. Package looks good.

2 minor things:

(1) The vignette says:

WhistleR can be installed from both bioconductor and github.

Please note that we strongly discourage installing Bioconductor packages from GitHub. Because of Bioconductor 6-month release cycles and because Bioconductor has a notion of release and devel, Bioconductor users should always use BiocManager::install() to install packages. This will spare them a lot of headaches with version mismatches. Please instruct your users to install the package with BiocManager::install() and do not encourage them to install from GitHub.

(2) You can do:
X <- makeGRangesFromDataFrame(X_df)
instead of:
X <- GRanges(seqnames = X_df[,1],
ranges = IRanges(start = X_df[,2],
end = X_df[,3]),
strand = X_df[,5])
Thanks, H.

Dear hpages,

Thank you very much for your review and comments. All of the 2 points are now implemented in the newest version (0.99.5).

With my best wishes, Zhen

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/WhistleR 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: ddaec1b9cfbf54ab4c81824e24870e21a3b38bdd

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/WhistleR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

hpages commented 3 years ago

Thanks for the changes.

I just realize now that WhistlerUsersGuide.pdf is a precompiled vignette and that the real vignette (Vignette_V_1.0.0.Rmd) is basically a pointer to the precompiled vignette. This is incompatible with Bioconductor guidelines.

The reason static/precompiled vignettes must be avoided is that there's no way to know when the code in them breaks. And the code in them will break at some point. Also this will happen sooner than you expect given that the package has 100+ dependencies (direct and indirect).

OTOH when the code in a real vignette (i.e. a vignette with code chunks that are evaluated by R CMD check) breaks, we will immediately know that, thanks to our daily checks. This is why providing a real vignette is a key feature of Bioconductor.

Thanks, H.

ZW-xjtlu commented 3 years ago

@hpages Thanks very much for your comment and explanations.

The real vignette will be added soon. However, I have 2 more questions: (1) Since the Machine learning package (H2O) I need to demonstrate is not installed on the Bioconductor server, can I add some key examples in the real vignette but also keep the precompiled WhistlerUsersGuide.pdf? (2) Can I at this stage change the name of the package?

Best wishes, Zhen

hpages commented 3 years ago

Hi @ZW-xjtlu ,

If your typical workflow requires CRAN package h2o, then this needs to be formally stated by listing h2o in your Suggests field. This will trigger automatic installation of h2o on the build machines.

As for renaming the package at this stage, I'm not sure what's the best way to do it. Maybe resubmit with a different name and explain the situation in the new submission? @lshep @vjcitn @nturaga Would that be ok or maybe there is an easier way? Thanks.

H.

nturaga commented 3 years ago

It’s easier to close this completely and open another one in my opinion.

Otherwise, the name change has to be done on the SPB and then the git ecosystem too.

vjcitn commented 3 years ago

The name should not be changed unless there is an extremely compelling reason.

hpages commented 3 years ago

Thanks Nitesh, Vince.

@nturaga @lshep If they resubmit with a different name, then I guess I'll change the status of this submission to "declined". Will this trigger automatic removal of Whistler from our git server or will this need to be handled manually? Thanks

lshep commented 3 years ago

As far as I know there is no auto removal process and it would have to be removed manually by @nturaga

hpages commented 3 years ago

Any update on this @ZW-xjtlu ? Thanks

ZW-xjtlu commented 3 years ago

Dear Herve,

Sorry for the late reply; my time is mostly occupied by teaching recently. Thanks for your clarification on the situation, so I decide to re-submit the package using another name.

With my best wishes, Zhen

On Apr 9, 2021, at 5:28 PM, Hervé Pagès @.**@.>> wrote:

Any update on this @ZW-xjtluhttps://github.com/ZW-xjtlu ? Thanks

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lshep commented 3 years ago

@vjcitn @nturaga I believe this means we can delete this out of the git.bioconductor.org repository?

nturaga commented 3 years ago

I've removed it from git.bioconductor. Thanks!

Bioconductor / Contributions

Submitting Package WhistleR #1871