VCFArray

[Liubuntu]

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[bioc-issue-bot]

Hi @Liubuntu

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: VCFArray
Title: Representing on-disk / remote VCF files as array-like objects
Version: 0.99.0
Authors@R: c(
    person("Qian", "Liu", email = "[email protected]", role = c("aut", "cre")),	
    person("Martin", "Morgan", role = "aut"))	       
Description: VCFArray extends the DelayedArray to represent VCF data entries
    as array-like objects with on-disk / remote VCF file as backend. Data
    entries from VCF files, includeing info fields, FORMAT fields, and the
    fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray
    instances with different dimensions. 
biocViews: Infrastructure, DataRepresentation, Sequencing
Depends:
    R (>= 3.5),
    methods,
    BiocGenerics,
    DelayedArray (>= 0.7.28)
License: GPL-3
Encoding: UTF-8
URL: https://github.com/Liubuntu/VCFArray
BugReports: https://github.com/Liubuntu/VCFArray/issues
Imports:
    tools,
    GenomicRanges,
    VariantAnnotation (>= 1.27.7),
    GenomicFiles (>= 1.17.3),
    S4Vectors (>= 0.19.19),
    Rsamtools
RoxygenNote: 6.1.0
VignetteBuilder: knitr
Suggests:
    BiocStyle,
    BiocManager,
    testthat,
    knitr,
    rmarkdown

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[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: "skipped, ERROR".
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[lawremi]

Looks useful. I think the pos meta column in @gr could be formalized better, perhaps as its own slot, or via a validation rule.

[Liubuntu]

Thank you @lawremi for your input. I have made pos as its own slot now. Will come in next version after I fix the current error, (which should come from the dependency). Thanks!

Best,
Qian

[bioc-issue-bot]

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

28e0656 moving meta column pos in @gr out as a slot.

[bioc-issue-bot]

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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[bioc-issue-bot]

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

0cf016b check if exist the file path that are downloaded i...

[bioc-issue-bot]

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Your package has been built on Linux, Mac, and Windows.

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[bioc-issue-bot]

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

5b7c355 test vignette in building error.

[bioc-issue-bot]

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Your package has been built on Linux, Mac, and Windows.

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[bioc-issue-bot]

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

57eabd1 redo the rgstack example to clear the building err...

[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.

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[bioc-issue-bot]

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

6a5df1d adding VCFArray.Rproj into .gitignore

[bioc-issue-bot]

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This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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[bioc-issue-bot]

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

2599f8a git rm VCFArray.Rproj

[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.
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]

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

2734425 don't examples of rgstack to save checking time.

[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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[Liubuntu]

Hi @Kayla-Morrell,

I have modified the package to pass building and checks on all platforms. One example for RangedVcfStack was deactivated in man/VCFArray-class.Rd, because it takes longer time to give the "TIMEOUT" warning on windows system. However the same examples has been included in vignette with eval = TRUE, and also been tested in test/testthat/test_VCFArray.R. So there won't be any problem in evaluating.

So I think it's ready for a review. Please let me know if there any further issues I need to address. Thank you very much!

Best,
Qian

[Kayla-Morrell]

Hi @Liubuntu

Your package looks good to me, I just had a few minor things to bring to your attention. Please see the initial review below:

Vignette

• REQUIRED: under 3.1, I try to run code for the remote VCF file, but I come up with an error when I try to define va. Double check that this code is able to be executed even if it isn't evaluated in the vignette. See the error below:

Error in vcfFields(file) : all(file.exists(x)) is not TRUE

• SUGGESTION: under 3.2.1, there doesn't need to be a period after "slot accessors" since none of the other headers have a period after them.

R files

• SUGGESTION: AllUtilities.R, for .header() you might consider taking out the FIXME comment.
• SUGGESTION: AllUtilities.R, for .get_VCFArraySeed_type() you might consider a closing edge case of some kind. Either closing with a final else statement or using stopifnot().
• SUGGESTION: AllUtilites.R for .get_VCFArrarySeed_basic_param() the same as the previous suggestion with a closing edge case.
• REQUIRED: VCFArray-classes.R for the VCFArray constructor setMethod() the comment about extract_array should be removed.

man files

• REQUIRED: VCFArray-classes.Rd I tried running the \dontrun{} section of examples and I get an error when trying to assign stack and the rest of the example can't be evaluated. The error is below:

Error in validObject(.Object): invalid class "VcfStack" object: all rownames(object) must be in seqlevels(object)

inst files

• REQUIRED: todo.Rmd should be removed.

tests

• SUGGESTION: for XStringSetList, IntegerList... there is a comment that could be potentially good tests. You might consider developing these.
• REQUIRED: for RangedVcfStack geno() get rid of the "success" comment.

Comment back with updates that have been made and when the package is ready for a re-review.

Best,
Kayla

[bioc-issue-bot]

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

4fdc761 removing the script in generating rgstack example

[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: "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.

[bioc-issue-bot]

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

2da5841 using a small rgstack example

[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.

[Liubuntu]

Hi @Kayla-Morrell ,

The "WARNING" for windows checking has been cleared! So finally ready for the 2nd review. :)

Best,
Qian

[Kayla-Morrell]

Hi @Liubuntu,

All the updates look great. I'm working through my 2nd review and should have some comments for you soon.

Thanks,
Kayla

[Kayla-Morrell]

Thank you @Liubuntu for making the necessary changes. Below are my comments:

REQUIRED: VCFArray-classes.R for the VCFArray constructor
setMethod() the comment about extract_array should be removed.

Can you point out which specific line is it? sorry that I couldn't be
able to locate...

It would be line 244 in VCFArray-classes.R.

man files
REQUIRED: VCFArray-classes.Rd I tried running the \dontrun{} section
of examples and I get an error when trying to assign stack and the
rest of the example can't be evaluated. The error is below:
Error in validObject(.Object): invalid class "VcfStack" object: all
rownames(object) must be in seqlevels(object)

I could not reproduce this error, I wonder if you are using a version
of GenomicFiles >= 1.17.3? because the example of generating stack
and rgstack is mostly copied from the example in ?VcfStack, which
should works since the packages are building without error.

This was my mistake. I was trying to perform the example directly from the .Rd file instead of looking at the formatted man page. When doing it from the .Rd file I was getting an error due to the definition of the names of files ("\\\\1"). This formats correctly and when going through the example on the proper man page I don't get the the error. So this requirement can be ignored.

Once the first comment is addressed I'll be ready to accept your package.

Thank you,
Kayla

[bioc-issue-bot]

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

6e93575 remove redundant comments

[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.
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]

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

55e61c2 make vcfstack example further smaller

[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".
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]

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

3aa9027 fix test dim values for rgstack file

[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.

[Liubuntu]

Hi @Kayla-Morrell ,

The comment was removed for the first issue and the building report is cleared. Thanks!

Best,
Qian

[bioc-issue-bot]

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]

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

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