IMAS

[hangost]

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[bioc-issue-bot]

Hi @hangost

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: IMAS
Type: Package
Title: Integrative analysis of Multi-omics data for Alternative Splicing
Version: 0.99.0
Author: Seonggyun Han, Younghee Lee
Maintainer: Seonggyun Han <hangost@ssu.ac.kr>
Description: Integrative analysis of Multi-omics data for Alternative splicing.
License: GPL-2
Depends: R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
Imports: doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
         foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats,
         ggfortify, grDevices, methods, Matrix, utils, graphics,
         gridExtra, grid, lattice, Rsamtools, survival, BiocParallel
Suggests: BiocStyle, RUnit
biocViews: AlternativeSplicing, DifferentialExpression,
        DifferentialSplicing, GeneExpression, GeneRegulation,
        Regression, RNASeq, Sequencing, SNP, Software, Transcription

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170308183125.html

[lawremi]

It seems this could make better use of the GenomicAlignments package. Custom CIGAR parsing code, looping over individual reads, etc, are red flags.

[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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170309080803.html

[lshep]

Thank you for your submission. Please see the following:

GENERAL:

• [ ] It would help to shorten lines to 80 characters so you could read them when accessing via web browswer on github
• [ ] Please address @lawremi comments above. There seems to be similar functionality already provided in GenomicAlignments - Either genomicAlignments should be used or please give details on how the functionality differ.

VIGNETTE:

• [ ] Add installation instructions to vignette also.
• [ ] Save output when creating visualization to a tempdir()

MAN PAGES:

• [ ] perhaps a cleaner way in examples than a bunch of commented out code is dontrun{} for sections of code that should not be executed
• [ ] you don't run any of your functions in the examples ... why?
• [ ] for your sample data more information on how the data was generated and where the data was generated - not just that it is provided with the package.
• [ ] IMAS-package.Rd - expand on details, suggest or list the main functions for use, give a workflow example
• [ ] test - delete

R code:

• [ ] Avoid use of 1:n; use seq_len(n) or seq_along(x) instead. this is also true for 1:nrow() etc. and problems when nrow() == 0; use seq_len(nrow()) instead.
• [ ] preallocate when necessary- See: http://bioconductor.org/developers/how-to/efficient-code/
• [ ] (Optional) Use BiocParallel rather than foreach; it provides users with a more consistent experience in the Bioconductor universe.

After updates have been made please comment back here with how the above issues have been addressed. Thank you.

[lshep]

As we are nearing the next release (release schedule) I wanted to check in to see if you had any questions or comments. We would love to be able to include your package in the next release if we can get it through the review process. Please address the above issues and comment back here with how they have been addressed or any questions or concerns you are encountering.

[hangost]

Dear reviewers, We sincerely appreciate for considering our R package entitled “IMAS: Integrative Analysis of Multi-omics data for Alternative Splicing”. We agreed with and addressed the comments and suggestions from the reviewers. We submitted the point-by-point response to those comments with revised source codes: GENERAL:

1. It would help to shorten lines to 80 characters so you could read them when accessing via web browswer on github
   • We thoroughly modified to shorten lines to 80 characters in source codes, but do I need to do them in NAMESPACE, manual, and etc. as well?
2. Please address @lawremi comments above. There seems to be similar functionality already provided in GenomicAlignments - Either genomicAlignments should be used or please give details on how the functionality differ.
   • We modified source codes to use the extractAlignmentRangesOnReference function in the GenomicAlignments package and the cigarParsing.R function was removed. In addition, we used the readGAlignments function in the GenomicAlignments package, instead of the ReadBamToPosition.R function to extract reads from bam files.

VIGNETTE:

1. Add installation instructions to vignette also.
   • We added the installation instructions to vignette.
2. Save output when creating visualization to a tempdir()
   • we modified a source code to add the option of save output.

MAN PAGES:

1. perhaps a cleaner way in examples than a bunch of commented out code is dontrun{} for sections of code that should not be executed
   • we modified a source code to make an example clear.
2. you don't run any of your functions in the examples ... why?
   • The visualization is the last step of the package workflow. Since the function ASvisualization.R for the visualization performs every example in other analysis functions such as, ClinicAnalysis.R, MEsQTLFinder.R, and etc.. The example in other functions without the ASvisualization.R can be redundant.
3. for your sample data more information on how the data was generated and where the data was generated - not just that it is provided with the package.
   • We added more information to clearly explain the example data.
4. IMAS-package.Rd - expand on details, suggest or list the main functions for use, give a workflow example
   • We added more information for the workflow example.
5. test – delete
   • We deleted.

R code:

1. Avoid use of 1:n; use seq_len(n) or seq_along(x) instead. this is also true for 1:nrow() etc. and problems when nrow() == 0; use seq_len(nrow()) instead.
   • We thoroughly modified source codes to use seq_along and seq_len, instead of 1:n, 1:nrow(), nrow, and etc.
2. You also use a lot of applys - preallocate - See: http://bioconductor.org/developers/how-to/efficient-code/
   • We modified source codes to minimally use applys, and preallocate variables.
3. (Optional) Use BiocParallel rather than foreach; it provides users with a more consistent experience in the Bioconductor universe.
   • We modified source codes to use BiocParallel instead of foreach, and this can be applied after this update.

Thanks.

[lshep]

Could you please make sure your webhook is set up properly. Normallly when the webhook is initialized the automatic build will happen with a version bump. I'll kick off a manual build this time but please check. I will review and get back soon with any other feedback

[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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170330073851.html

[lshep]

Could you please look into the windows ERROR that is occurring.

[hangost]

Thank you very much for your feedbacks!!! I will check the error.

Thanks!

[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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170403074259.html

[lshep]

Ignore this ERROR for now. I will review the package and get back to you shortly with any other comments

[bioc-issue-bot]

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

804ce20 Add files via upload

[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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170404042400.html

[lshep]

There is still an ERROR on tokay2 that needs to be addressed. I can reproduce it and it occurs as specified in code chunk number 12: Splicingfinder function when running ExonsCluster(ASdb, transdb).

Here is the traceback()

> traceback()
5: stop(simpleError(msg, call = expr))
4: e$fun(obj, substitute(ex), parent.frame(), e$data)
3: foreach(alt.num = seq_along(alt.gene), .packages = called.packages,
       .combine = rbind) %dopar% {
       over.num <- Alt.mat[, "EnsID"] == alt.gene[alt.num]
       Alt.mat <- rbind(Alt.mat[over.num, ])
       if (alt.type == "ES") {
           each.result <- rbind(ES.Alt.result(Alt.mat))
       }
       else if (alt.type == "ASS") {
           each.result <- rbind(ASS.Alt.result(Alt.mat))
       }
       else if (alt.type == "IR") {
           each.result <- rbind(IR.Alt.result(Alt.mat))
       }
       spl.nums <- grep("Spl|spl", colnames(each.result))
       e.chr <- unique(Alt.mat[, "Nchr"])
       each.result <- rbind(each.result[, -spl.nums])
       each.result <- cbind(EnsID = alt.gene[alt.num], Nchr = e.chr,
           Strand = unique(Alt.mat[, "Strand"]), each.result)
       each.result
   }
2: for.f(each.mat, ES.gene, "ES")
1: ExonsCluster(ASdb, transdb)

When I debug a little further is seems to fail:

debug: each.mat <- Alt.splice.result$ES
Browse[2]>
debug: each.re <- for.f(each.mat, ES.gene, "ES")
Browse[2]>
Error in { : task 1 failed - "could not find function "ES.Alt.result""

I hope this helps a little for you to debug the issue.

[bioc-issue-bot]

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

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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". 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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170404111456.html

[bioc-issue-bot]

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

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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". 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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170404113247.html

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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". 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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170404155533.html

[bioc-issue-bot]

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

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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". 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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170404211738.html

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

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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". 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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170404222724.html

[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.

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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170404223806.html

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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". 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 following build report for more details:

http://bioconductor.org/spb_reports/IMAS_buildreport_20170405015144.html

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

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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". 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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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.

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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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[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.

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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". 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: "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.

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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". 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,

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

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