GuidoBarzaghi 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/GuidoBarzaghi/SingleMoleculeFootprintingData

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

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bioc-issue-bot commented 3 years ago

Hi @GuidoBarzaghi

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: SingleMoleculeFootprintingData
Type: Package
Title: Data supporting the SingleMoleculeFootprinting pkg
Version: 0.99.0
Authors@R: c(
    person(given = "Guido",
 family = "Barzaghi",
 role = c("aut", "cre"),
 email = "guido.barzaghi@embl.de",
 comment = c(ORCID = "0000-0001-6066-3920")),
    person(given = "Arnaud",
 family = "Krebs",
 role = c("aut"),
 email = "arnaud.krebs@embl.de",
 comment = c(ORCID = "0000-0001-7999-6127")),
    person(given = "Mike",
 family = "Smith",
 role = c("ctb"),
 email = "mike.smith@embl.de",
 comment = c(ORCID = "0000-0002-7800-3848"))
    )
Description: This Data package contains r objcets necessary to run some of the
    functions from the SingleMoleculeFootprinting package. 
    SingleMoleculeFootprinting is an R package providing functions 
    to analyze Single Molecule Footprinting (SMF) data.
biocViews: 
    ExperimentHub, ExperimentData, SequencingData
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports:
    ExperimentHub,
    utils
Suggests: 
    knitr,
    rmarkdown,
    QuasR,
    GenomicRanges,
    BSgenome.Mmusculus.UCSC.mm10
VignetteBuilder: knitr
RoxygenNote: 7.1.1

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

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GuidoBarzaghi commented 3 years ago

AdditionalPackage: https://github.com/GuidoBarzaghi/SingleMoleculeFootprinting

bioc-issue-bot commented 3 years ago

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

GuidoBarzaghi commented 3 years ago

Hi @LiNk-NY,

I was wondering whether I misunderstood the procedure for submitting an additional package. I was expecting for it to automatically go through the build checks analogously to what happened to the primary one. Is there something I did wrong that is causing the system not to be prompted?

bioc-issue-bot commented 3 years ago

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LiNk-NY commented 3 years ago

Hi Guido, @GuidoBarzaghi It looks like the procedure to add the package worked out smoothly. Please see the result report and modify accordingly.

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bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

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GuidoBarzaghi commented 3 years ago

@LiNk-NY thanks a lot for your reply. This is my first ever submission to Bioconductor so I'm not entirely sure on what to expect at each step.

I'm afraid I need to ask for your input again: there is an ERROR reported under the "tokay2 BUILD BIN output" section that I'm not sure how to tackle. I'm not entirely sure how I can influence the installation of dependencies on windows. Do you have any suggestion?

grimbough commented 3 years ago

@GuidoBarzaghi It looks like Rbowtie & subsequently QuasR aren't available for 32-bit Windows. You can specify not to build your package on that platform by adding the file .BBSoptions to the root of your package. It should be fine to copy the one from QuasR at https://github.com/fmicompbio/QuasR/blob/master/.BBSoptions

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GuidoBarzaghi commented 3 years ago

@grimbough Oh I see. Thank you for clarifying!

bioc-issue-bot commented 3 years ago

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LiNk-NY commented 3 years ago

Hi Guido, @GuidoBarzaghi

Thank you for your submission. Please see the reviews below. Feel free to comment with questions.

Best regards, Marcel

SingleMoleculeFootprinting #2034

DESCRIPTION

Please use full sentences in the Description field (for BiocCheck).
Do you need to import both AnnotationHub and ExperimentHub?
Most often, the data package goes in the Suggests field.
Make LazyData: false or remove the line.
Add a BugReports field.

NAMESPACE

AnnotationHub seems out of place.
Perhaps the parallel functionality listed here is for user-level commands?
Everything else looks good.

vignettes

Please stick to the 80 width character limit convention. It makes it easier to read and review.
Load the packages that you use with library(parallel), for example.
Avoid using eval = FALSE in code chunks. Use an small example dataset to show the functionality of your package. eval=FALSE chunks can become stale quite quickly.
Why are \ backslashes needed in the text?
I suggest moving the Installation section to the beginning of the vignette.
Remove the GitHub installation section.
The AnnotationHub query is not necessary when you already have a data package that has a covenience function for loading the data. Use your own package.
Please don't move the file and keep it in the default cache. Otherwise, your package will be downloading the data every time it gets checked on our build system (BBS).
Perhaps you can provide a runnable qQCReport with a small dataset?
Avoid 1:n sequence generation, use the more robust seq_len(n).
Do not use print even in the vignette. Use message if necessary.
Provide a sessionInfo at the end of the vignette.

Minor:

Our convention is to use <- for assignment instead of = but this not strictly enforced.
There are some typos chuck > chunk

R

You can use the data package for your examples, if necessary. Avoid using the tempdir() especially for downloaded data as pointed out above.

Some of the logic can be improved, for example:

MethSM_minus = MethSM[apply(MethSM[,IsMinusStrand], 1, function(i){sum(is.na(i)) != length(i)}) > 0, IsMinusStrand]
MethSM_plus = MethSM[apply(MethSM[,!IsMinusStrand], 1, function(i){sum(is.na(i)) != length(i)}) > 0, !IsMinusStrand]

It's not clear in the code what you're trying to do. Perhaps !all(is.na(i)) is what you need to check for each row? or rowSums(is.na(i)) > 0? These are likely to be faster.

Add a verbose argument to functions like CallContextMethylation and others.
Where possible, avoid numeric indices and use named indices.
Consider using BiocParallel instead of parallel::makeCluster for BaitCapture. It may work better across systems.
SampleCorrelation should be using data in the extdata directory.
Avoid saving the file for the user in SampleCorrelation, create the plot and display it in the graphics device. The user will then be able to choose their format of choice (e.g., png).

tests

We highly recommend adding unit tests to your package.

SingleMoleculeFootprintingData

DESCRIPTION

Please include more information in the Description field.

vignette

Show the user how to download the data for the package by calling the function created by createHubAccessor.

LiNk-NY commented 3 years ago

Note. For more information, see:

BiocCheck::BiocCheck("SingleMoleculeFootprinting")

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bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

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GuidoBarzaghi commented 3 years ago

@LiNk-NY thanks a lot for your comments. I have tried to thoroughly address all the points you brought up.

I would just like to offer some clarifications about a couple of them:

DESCRIPTION:

Most often, the data package goes in the Suggests field.

In this case, some of the objects accessed through the data package are necessary for a couple of functions to work. Therefore it is necessary to import the data package when loading the software one

VIGNETTE:

Please don't move the file and keep it in the default cache. Otherwise, your package will be downloading the data every time it gets checked on our build system (BBS).

I actually just copy it in order to rename it with a relevant extension. This is necessary for one of the dependencies of SingleMoleculeFootprinting to recognise these files.

Perhaps you can provide a runnable qQCReport with a small dataset?

Unfortunately, qQCreport will not run with a dataset that is too small (such is the case for the example data provided through SingleMoleculeFootprintingData). Consequently, I removed the code chunk relative to this and referred to the documentation of the package QuasR relative to the function qQCreport.

R:

Consider using BiocParallel instead of parallel::makeCluster for BaitCapture. It may work better across systems.

Because of this and other comments, I removed all the instances of makeCluster/stopCluster across the package and leave to the user the choice of how to create a cluster object. Still in the vignette and the example code in the function manuals I show how to do this using parallel since this is how the documentation of the dependency QuasR indicates.

Where possible, avoid numeric indices and use named indices.

Unfortunately where numeric indices are still present they are strictly necessary as of now, I will keep this in mind for the future.

Once again, thanks for your suggestions I will keep them in mind as I go along and keep developing in the future. Let me know if I can further clarify something.

LiNk-NY commented 3 years ago

Hi Guido, @GuidoBarzaghi

DESCRIPTION:

Most often, the data package goes in the Suggests field.

In this case, some of the objects accessed through the data package are necessary for a couple of functions to work. Therefore it is necessary to import the data package when loading the software one

I would not require everyone to install data package. Only the users using those functions should install the data package. You can implement this using some logic to check for the package availability (after putting the package in Suggests):

if (!requireNamespace("LargeDataPackage", quietly = TRUE))
    stop("Install the 'LargeDataPackage' to use this function")

VIGNETTE:

Please don't move the file and keep it in the default cache. Otherwise, your package will be downloading the data every time it gets checked on our build system (BBS).

I actually just copy it in order to rename it with a relevant extension. This is necessary for one of the dependencies of SingleMoleculeFootprinting to recognise these files.

I see the issue now. I think the software should work regardless of the extension but you don't have any control of QuasR... I will ask about a way to preserve the file extension.

Thanks! Best, Marcel

Bioconductor / Contributions

SingleMoleculeFootprintingData #2034

SingleMoleculeFootprinting #2034

DESCRIPTION

NAMESPACE

vignettes

R

tests

SingleMoleculeFootprintingData

DESCRIPTION

vignette

DESCRIPTION:

VIGNETTE:

R:

DESCRIPTION:

VIGNETTE: