igvR

[paul-shannon]

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[bioc-issue-bot]

Hi @paul-shannon

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: igvR
Type: Package
Title: igvR: integrated genomics viewer
Version: 0.99.18
Date: 2018-04-13
Author: Paul Shannon
Maintainer: Paul Shannon <paul.thurmond.shannon@gmail.com>
Depends: R (>= 3.4.0), GenomicRanges, VariantAnnotation, rtracklayer, BrowserViz (>= 2.0)
Imports: methods, BiocGenerics, httpuv, utils
Suggests: RUnit, BiocStyle, knitr, rmarkdown
Description: Access to igv.js, the Integrated Genomics Viewer running in a web browser.
License: MIT + file LICENSE
LazyLoad: yes
biocViews: Visualization, ThirdPartyClient
Collate:
   'utils.R'
   'Track.R'
   'AnnotationTrack.R'
   'UCSCBedAnnotationTrack.R'
   'DataFrameAnnotationTrack.R'
   'VariantTrack.R'
   'QuantitativeTrack.R'
   'DataFrameQuantitativeTrack.R'
   'UCSCBedGraphQuantitativeTrack.R'
   'GRangesAnnotationTrack.R'
   'GRangesQuantitativeTrack.R'
   'igvR.R'
NeedsCompilation: no
Packaged: 2018-03-22 20:02:10 UTC; paul
VignetteBuilder:
  knitr
RoxygenNote: 6.0.1

[bioc-issue-bot]

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

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

257fc34 version bump to trigger build, webhook added

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[bioc-issue-bot]

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[bioc-issue-bot]

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[bioc-issue-bot]

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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.

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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: "ABNORMAL". 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.

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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: "ABNORMAL". 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.

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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: "ABNORMAL". 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]

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: "ABNORMAL". 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.

[dvantwisk]

Hello,

I am taking over this package review for Herve. I will review it promptly once the builds read OK.

[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: "ABNORMAL". 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.

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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: "ABNORMAL". 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.

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[bioc-issue-bot]

Dear Package contributor,

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

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[bioc-issue-bot]

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

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[bioc-issue-bot]

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[bioc-issue-bot]

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[bioc-issue-bot]

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[bioc-issue-bot]

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

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[bioc-issue-bot]

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[bioc-issue-bot]

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[bioc-issue-bot]

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

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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: "ABNORMAL". 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.

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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: "ABNORMAL". 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]

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: "ABNORMAL". 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.

[paul-shannon]

Hi Daniel, Thanks for offering to review my package. May I offer a little history? I submitted IGV on April 1st, naively thinking that the old support for web browsers in the build system - which Dan Tenenbaum created and maintained when we were both on the core team - was still in place. My questions about that to bioc-devel went unanswered for days. Quite frustrating. Vince Carey eventually helped out, for which I was grateful.

The package has built clean for several days now. I just changed the name from IGV to igvR, created this new issue, added the webhook, and now I get an endless stream of "ABNORMAL build" messages.

I am pretty sure I need your help with this. It may be my stupid error. It might even be the build system. The infinite "ABNORMAL build" loop doesn't seem like it is entirely my fault :}

If you wait till a green build occurs before trying to help I predict we will never get there!

• Paul

[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: "ABNORMAL". 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]

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: "ABNORMAL". 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]

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: "ABNORMAL". 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.

[dvantwisk]

I see. This is bizarre behavior by our build machines. We will look into it.

[paul-shannon]

Cool. Thanks!

On Apr 13, 2018, at 11:37 AM, Daniel Van Twisk notifications@github.com wrote:

I see. This is bizarre behavior by our build machines. We will look into it.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[bioc-issue-bot]

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

2a72d82 eval=FALSE again in markdown vignette

[bioc-issue-bot]

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

2a72d82 eval=FALSE again in markdown vignette

[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, TIMEOUT". 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.

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[bioc-issue-bot]

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

8c770dc corrected 'integrated' to 'integrative'

[bioc-issue-bot]

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

8c770dc corrected 'integrated' to 'integrative'

[dvantwisk]

@paul-shannon A reason for this issue may be that you have multiple web-hooks on this issue. Can you check if you do, and if so, correct this?

[paul-shannon]

@dvantwisk Just one now. My mistake.

[bioc-issue-bot]

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

df40ca6 version bump, trigger build

[bioc-issue-bot]

Dear Package contributor,

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[bioc-issue-bot]

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

4905bc9 R > 3.5.0

[bioc-issue-bot]

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Congratulations! The package built without errors or warnings on all platforms.

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[dvantwisk]

Here's a review for your package. Please address the following issues and message me back when your are done. I may have some more thing to say about the file R/igvR.R but I'd like to check in on a few things before then. You are on track for having your package included in the 3.7 release.

.gitignore

• [REQUIRED] add IGV.Rproj, igvR.Rprog, build.makefile, and NAMESPACE.oldManuallyCreated to .gitignore.

R/GENERAL

• [CONSIDER] Be specific with what classes are being input and output. For example, AnnotationTrack.R:L15 it seems that the @param soureType is asking for a character argument git there are packages like rtracklayer that have specific classes for files. In general, it is advisable to be as specific as possible regarding input and output for the user.

R/AnnotationTrack.R

• [CONSIDER] L58: Use match.arg() to improve style of function declaration. For example, the parameter displayMode can have three values "COLLAPSED", "EXPANDED", and "SQUISHED". The parameter in the function declaration can be written as displayMode=c("SQUISHED", "COLLAPSED", "EXPANDED"). The value that the user uses can be obtained with displayMode <- match.arg(displayMode). The first value (in this case "SQUISHED") is the default argument. Using this method makes it clear to users what the allowed inputs to a function are and may also make error catching easier. There are many places in this package that you could use this.

R/Track.R

• [REQUIRED] this package is trying to set the getInfo and get getSize. These names seem rather "general" and it isn't ideal for the structure of the Bioconductor project to have them implemented here. I ask that you either:
  • Change the name to be more specific like trackinfo and tracksize.
  • Find existing Generics in a high level package and setMethod for a signature consisting of the Track class.

R/utils.R

• [REQUIRED] it seems that printf() is only being used to display messages to the user, correct? If so, then replace print() in the function with message(), as message()'s purpose is to display diagnostic messages and can be toggled by the user; this isn't the case with print(). Also, I don't see the need to export this small utility function (developers or users probably aren't coming to the package to use printf()), so please remove the @export tag.

[bioc-issue-bot]

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

e543f3a implemented all but one suggestion from @dvantwisk

[paul-shannon]

@dvantwisk Thank you for your suggestions - they all make sense, all are now implemented but for one, which I think I can explain to your satisfaction:

[CONSIDER] Be specific with what classes are being input and output. For
example, AnnotationTrack.R:L15 it seems that the @param soureType is asking
for a character argument git there are packages like rtracklayer that have
specific classes for files. In general, it is advisable to be as specific as
possible regarding input and output for the user.

The sourceType parameter to the AnnotationTrack constructor includes these three possibilities from the igv.js ontology (I only support the first one for now):

• file
  • gcs (Google Cloud Storage)
  • ga4gh (the Global Alliance API)

I think that Michael's variety of specific file types in rtracklayer do not actually apply here. The three options listed above are perhaps better understood as protocols with which to obtain data, and a generic file type is, I believe, the proper abstraction.