scanMiR

[fridoling]

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[bioc-issue-bot]

Hi @fridoling

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: scanMiR
Type: Package
Title: scanMiR
Version: 0.99.11
Depends: R (>= 4.0)
Date: 2021-04-20
Authors@R: c(
    person("Pierre-Luc", "Germain", email="pierre-luc.germain@hest.ethz.ch", 
  role=c("cre","aut"), comment=c(ORCID="0000-0003-3418-4218")),
    person("Michael", "Soutschek", email="michael.soutschek@hest.ethz.ch", role="aut"),
    person("Fridolin", "Gross", email="fridolin.gross@hest.ethz.ch", role="aut"))
Imports:
    Biostrings,
    GenomicRanges,
    IRanges,
    data.table,
    BiocParallel,
    methods,
    GenomeInfoDb,
    S4Vectors,
    ggplot2,
    stats,
    stringi,
    utils,
    grid,
    gridExtra
Suggests: knitr, rmarkdown
Description:
    A set of tools for working with miRNA affinity models (KdModels),
    efficient scanning for miRNA binding sites, and predicting target 
    repression. It supports scanning using miRNA seeds, full miRNA sequences 
    (enabling 3' alignment) and KdModels, and includes the prediction of slicing
    and TDMD sites. Finally, it includes utility and plotting functions (e.g. 
    for the visual representation of miRNA-target alignemnt).
License: GPL-3
VignetteBuilder: knitr
RoxygenNote: 7.1.1
biocViews: miRNA, SequenceMatching

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Received a valid push on git.bioconductor.org; starting a build for commit id: 91c37c54fe0d0e31f3ad551705467a21c8b1e08e

[bioc-issue-bot]

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".
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Received a valid push on git.bioconductor.org; starting a build for commit id: 4de2d050327c75348479b4c3387f9067c2796e93

[bioc-issue-bot]

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".
This may mean there is a problem with the package that you need to fix.
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Please see the build report for more details. This link will be active
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[plger]

Hi @hpages, honored to have you as reviewer ;)
We had initially planned to add a companion ExperimentData package to the submission via AdditionalPackage, namely https://github.com/ETHZ-INS/scanMiRData , however BiocCheck on scanMiRData gives a warning due to the size of some of the RData files (which are ~3, ~8 and ~12 Mb). Each object contains a KdModelList (a class defined by scanMiR) containing the affinity data of all miRNAs.
Can we submit this here as a traditional ExperimentData package, despite the warning? Or must it be transformed into an ExperimentHub package?
Thanks in advance for the help,
Pierre-Luc & Fridolin

[hpages]

Hi @plger ,

I would need to be able to take a look at those files in scanMiRData to provide some advice but unfortunately the link you provided doesn't work. Can you fix it?

Thanks,
H.

[plger]

sorry @hpages , I thought it was public already... now the link should work

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Received a valid push on git.bioconductor.org; starting a build for commit id: fe6898fd29d9b94c36ce48fbb7d42c529f12cd3d

[bioc-issue-bot]

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, WARNINGS, skipped".
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,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: f0db8b4d0d0725dff83cc94e4aab2d8320447d1c

[bioc-issue-bot]

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, WARNINGS, skipped".
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,
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git@git.bioconductor.org:packages/scanMiR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Received a valid push on git.bioconductor.org; starting a build for commit id: 20fa1e747aa1912960e212399697374bac78d562

[bioc-issue-bot]

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[hpages]

Hi @plger ,

scanMiRData_0.99.2.tar.gz is 23M which maybe is a little bit more than what we usually recommend for a data experiment package, so moving the datasets to ExperimentHub would make sense. However it's not crazy big either so we can work with that, at least for now. And since the 3 datasets are serialized instances of a new S4 class that is part of the submission (the KdModelList class), I actually think that it's going to be easier if the datasets live in the data package and not on ExperimentHub. Just in case the design of the S4 class changes during the review process (in which case updating the serialized datasets is going to be easier if they live in the package).

So yes, please submit scanMiRData as an additional package.

Thanks,
H.

[fridoling]

AdditionalPackage: https://github.com/ETHZ-INS/scanMiRData

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Received a valid push on git.bioconductor.org; starting a build for commit id: 44ccd363f71596969fd7feffa6fa507f406a4c41

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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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Or it may mean that there is a problem with the build system itself.

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Remember: if you submitted your package after July 7th, 2020,
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Received a valid push on git.bioconductor.org; starting a build for commit id: 66f62cecbdec0e67aff86b683c1cd0089ac65cf9

[bioc-issue-bot]

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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Received a valid push on git.bioconductor.org; starting a build for commit id: ba2ccd9e7e2a5534f3ec2b745a6f1cab1de76d28

[bioc-issue-bot]

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

[bioc-issue-bot]

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

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b2c1b7fbf1437c131a55bdcdf91527e2c4064cb1

[bioc-issue-bot]

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

[plger]

@hpages we've got a third (and last!) package ( https://github.com/ETHZ-INS/scanMiRApp ) depending on scanMiR. It's the dependency-heavy one, containing wrappers & extras & a shiny app... should we add it here again, or maybe wait for this review to be over and start a fresh new one after?

[lshep]

Sorry for the delay. If it is a related package that uses scanMiR or scanMirData than I would say it is okay to add it here as an AdditionalPackage. Cheers

[vjcitn]

This package is in good shape. I think it would be good to address BiocCheck events:

 [3] "Consider adding these automatically suggested biocViews: Alignment"                                                                                                                
 [4] " Avoid 1:...; use seq_len() or seq_along()"                                                                                                                                        
 ...                                                                                                                                     
 [6] "Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."                                                                         
 [7] "Consider adding unit tests. We strongly encourage them. See\n  http://bioconductor.org/developers/how-to/unitTesting-guidelines/."  

specifically the unit test suggestion is important; if you don't want to do it please indicate why.

[vjcitn]

I also took the liberty of trying out the app. I used the example and was able to generate

Warning: Error in dots_list: argument "subtitle" is missing, with no default
  [No stack trace available]
Warning: The 'plotly_click' event tied a source ID of 'manhattan' is not registered. In order to obtain this event data, please add `event_register(p, 'plotly_click')` to the plot (`p`) that you wish to obtain event data from.
'select()' returned 1:1 mapping between keys and columns

Do you want to address these?

[plger]

@vjcitn the two scanMiRApp warnings are now fixed.
For this one I'll be the maintainer, is that going to create permission conflicts if we add it through this issue? (@fridoling being the scanMiR maintainer... he'll also be addressing your above scanMiR-related queries)
Thanks

[lshep]

Honestly, I dont know if a different maintainer on an additionalpackage would cause an issue; my suspicion is yes we would run into permission issue. The catch with opening a new issue is if these accompanied packages are not accepted yet and in the official Bioconductor repository then the new issue will not be able to find the dependent package so there may be a delay in reviewing the newly opened issue

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 18ff3a09835c1b45c33f27940e2ad5dd4dd94ea1

[bioc-issue-bot]

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

[fridoling]

@vjcitn we have added "Alignment" to the biocViews, a NEWS file, and unit tests (> 70% code coverage). We have used 1:... only if ranges are defined by hardcoded digits, so this cannot possibly cause any problems.

[fridoling]

@lshep Thanks for the info. We are not in a hurry, so we can wait for the review of scanMiR to be finished and then open a new issue.

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[vjcitn]

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

https://bioconductor.org/packages/scanMiRData

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.