packFinder

[jackgisby]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/jackgisby/packFinder

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[bioc-issue-bot]

Hi @jackgisby

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: packFinder
Type: Package
Title: de novo Annotation of Pack-TYPE Transposable Elements
Version: 0.99.0
Authors@R: person(given = "Jack", family = "Gisby", role = c("aut", "cre"), email = "jackgisby@gmail.com")
Description: Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches. Sequences are input in DNAString format, and ranges are returned as a dataframe (in the format returned by as.dataframe(GRanges)).
License: GPL-2
Encoding: UTF-8
Depends:
    R (>= 4.0.0)
Imports: 
    Biostrings,
    GenomicRanges,
    kmer,
    ape,
    methods
Suggests:
    biomartr,
    knitr,
    rmarkdown,
    testthat,
    dendextend,
    biocViews,
    BiocCheck,
    BiocStyle
RoxygenNote: 6.1.1
VignetteBuilder: knitr
URL: https://github.com/jackgisby/packFinder
BugReports: https://github.com/jackgisby/packFinder/issues
biocViews: Genetics, SequenceMatching, Annotation

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[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:

f4f304d Bump Package Version 0.99.1

[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:

e9576a8 Update R Version R CMD Check: Dependence on R ver...

[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.

[bioc-issue-bot]

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

a9f1771 File path typo in readUc and readBlast6Out 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.

[jackgisby]

Hi @nturaga

Just to pre-empt the note in my package and the chunks that use eval=FALSE in my vignette:

While R/bioconductor was appropriate for the main elements of this package (searching for transposable elements by pattern matching (Biostrings) and representing the ranges of predicted elements (GenomicRanges)) I wasn't able to find a package in R that implemented VSEARCH style clustering.

This clustering/alignment step is optional and is the last step in the analysis, but requires installation and use of the vsearch command line tool (I've included instructions in the vignette for downloading/using vsearch if users wish to). Therefore I haven't included run-able examples and chunks in the examples and vignette, respectively. This can be installed on MacOS, Linux or Windows systems.

I reckoned this was the best method for implementing (optional) vsearch clustering functionality with the package - although I'm open to improvements or changes if this isn't acceptable for bioconductor submission.

Additionally, I initially tested the package on R 4.0.0 thinking the next bioconductor release had already occured - I may need to update my description to >=4.0.0 for the next cycle?

[nturaga]

Hi @jackgisby

Just an add-on to to my subsequent review. Your package downloads 1.1 GB from git when i try to clone it.

Your .git repo is bloated possibly because of data files you pushed into the repo at some point and deleted them later on. You can trim this by using https://stackoverflow.com/questions/2116778/reduce-git-repository-size. Or something like https://rtyley.github.io/bfg-repo-cleaner/.

This is not optimal as size for a bioconductor software repo.

Best,

Nitesh

[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:

5ea3880 Update version to 0.99.4

[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.

[jackgisby]

Hi @nturaga

Thanks for pointing that out, I've done as you suggested and the repo is now significantly smaller.

[nturaga]

Great, thanks a lot. I'll send in your review in the week.

On Sat, Nov 23, 2019 at 11:41 AM Jack Gisby notifications@github.com wrote:

Hi @nturaga https://github.com/nturaga

Thanks for pointing that out, I've done as you suggested and the repo is now significantly smaller.

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[nturaga]

packFinder review

Thank you for responding and reducing the size of the .git folder.

R CMD build

ok

R CMD INSTALL

ok

DESCRIPTION

• ok

NAMESPACE

• ok

vignette

• Good vignette. Although there are a few eval=FALSE code blocks. Do you intend to not run them? If so, why?

R

• This seems like a block of code, which I will not be able to understand 1 year from now if I had written it. I'm not sure why you are checking for "read" permission twice in this block. Some documentation would go a long way for both yourself, and the reviewer :D

      if (!is.null(file)) {
        if (!(file.access(file, 4) == 0) |
            !(file.access(file, 4) == 0) |
            !(file.access(file, 2) == 0)) {
            stop("file does not exist, or R does not 
                have read/write permissions")
        }

• identifyTirMatches.R , You can use the methods start instead of matches@ranges@start. Try to avoid using solt accessors like @ unless you absolutely need to. There are other similar instances where you do this, but it's possible to find functions in the BioStrings package which help you with this.

• In packAlign.R, Use file.path instead of this, it's more robust. you seem to have used it in other places.

  packMatchesFile <- paste0(saveFolder, "/packMatches.fasta")

• In packClust.R, add a message to this location saying you are saving in the current folder,

  if (is.null(saveFolder)) {
      message("Saving in the current folder: ", getwd())
      saveFolder <- getwd()
  }

man

• Good.

tests

• good

[bioc-issue-bot]

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

e01ef01 Improving code readability based on review a0ab760 Second set of changes for bioconductor package rev...

[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.

[jackgisby]

Hi @nturaga

Thanks for your review, I've provided an answer to each of your points below although I'm very happy to make further improvements if necessary.

• Non-evaluated chunks: I've removed one of the eval=false blocks and made it run-able. The first remaining block is for the installation of the package from bioconductor. The other two use the VSEARCH command line tool (via system2()) for clustering and alignment functions. While these aren't essential to the annotation pipeline of the package, we found them to be useful for identifying groups of transposons; I could not find an equivalent tool in R that clustered sequences with the same performance and accuracy - others were not able to separate transposons into the groups of our validation set. Therefore, if users wish to use the clustering functions, they need to make sure to have installed this command line tool (instructions available in the vignette/documentation). The vignette chunks and examples for these functions were disabled so the automated tests would run, however if the CL application is installed they will run and I have unit tests for these that I run separately to the other checks.
• Unclear code/double file check: I think this must have been a typo that I copied a few times, I've fixed this bit of code; I've also generally re-organised some of the functions and added some comments that will hopefully make parts more clear.
• Slot accessors: Switched out slot accessors, in all functions, for accessor methods.
• File paths: There were a few places where I had some odd file path paste0 statements that didn't make sense, I've switched these out to be more consistent using file.path.
• Wd save message: Have added the message you recommended for this, and similar, functions.

I've implemented the CL tool in the way I thought seemed optimal - it's an optional final step that is not necessary for the main annotation workflow; therefore, I felt it was best to allow users to install it when/if needed. However, I realise this may not be standard for bioconductor packages? If necessary, I'm happy to change how this part of the package works.

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

https://bioconductor.org/packages/packFinder

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.