ChIP-seq signal quantifier pipeline (CSSQ)

[ashwathkumar]

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• Repository: https://github.com/ashwathkumar/CSSQ

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[bioc-issue-bot]

Hi @ashwathkumar

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: CSSQ
Title: Chip-seq Signal Quantifier Pipeline
Version: 0.99.0
Authors@R: 
    person(given = "Ashwath",
 family = "Kumar",
 role = c("aut", "cre"),
 email = "akumar301@gatech.edu",
 comment = c(ORCID = "0000-0001-9106-6715"))
Description: his package is desgined to perform statistical analysis to
    identify statistically significant differentially bound regions between
    multiple groups of ChIP-seq dataset. 
License: Artistic-2.0
Encoding: UTF-8
biocViews: ChIPSeq, DifferentialPeakCalling,  Sequencing, Normalization
Depends: SummarizedExperiment, GenomicRanges, IRanges, S4Vectors
Imports: GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 6.1.99.9001

[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 build report for more details.

[bioc-issue-bot]

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

1b6ddb2 Fixed build error due to incorrect dimensions

[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:

aefac8f Updated version

[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:

eb680cd Updated man pages

[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:

9db49fd Updated Rd files

[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.

[ashwathkumar]

@dvantwisk Hi Daniel ! It seems the package has passed the initial automated tests. I would very much like your feedback on the package so i can make the recommended changes and get this rolling. Thanks a lot for your time !

[dvantwisk]

Got it. I should have a review for you sometime early next week.

[ashwathkumar]

Great ! Thanks a lot for taking time to review the package. Looking forward to your 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.

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

Please see the build report for more details.

[dvantwisk]

I apologize for the wait!

Here is a review of your package. [REQUIRED] tags are changes that must be made or addressed. [CONSIDER] tags are changes that are advisable but not required. Message me back when you are done making changes.

R/GENERAL:

• [REQUIRED] Your documentation should say when a parameter uses a default
  values if the user does not give input. Many parameters that are documented
  throughout you package do not include documentation regarding default values.
• [CONSIDER] I've noticed that you end each line with ;. This is common
  in more strongly-typed languages like C but R doesn't require it and most
  R-programmers generally don't do this. Mind you, it's not incorrect to use ;,
  it's just not commonly done as it's another unnecessary key stroke.

R/dbAnalyze.R

• [REQUIRED] Does the comparison parameter work when it is assigned its
  default value of c()? Does the result have any value to the user? Perhaps it's
  better to make comparison required and stop() if the user doesn't include
  it.

R/getBgSubVal.R

• [CONSIDER] Use match.arg() to declare countMode. There appears to be
  only four values that countMode can take. In the function declaration, you can
  write
  countMode = c('Union', 'IntersectionNotEmpty', 'IntersectionStrict', 'user supplied function')
  The first value is the default value of countMode, in this case it is Union.
  To obtain the user's input, you can write countMode <- match.arg(countMode) in
  the body of the function. Doing this makes it easier for the user to understand
  what values countMode can have. It also throws an error if the user gives
  anything other than the listed values. This can be done elsewhere in this
  package.

R/getRegionCounts.R

• [REQUIRED] L47: Use message() instead of print() to display diagnostic
  messages to the user. message() is preferable because they can be toggled off
  with suppressMessages().

R/loadCountData.R

• [CONSIDER] L34: The rtracklayer package has a method called
  import.bed() that is meant to import bed files. This is better to use than
  read.table().

R/plotDist.R

• [REQUIRED] It is preferable to return the plots that are generated to
  users using plotDist() instead of automatically placing them in a pdf. This
  allows the user control on how they want to display these plots. Perhaps this
  function should be user facing to allow users the ability to create their own
  plots?

R/preprocess.R

• [REQUIRED] It's somewhat confusing to may the default value of
  inputCountData to 'None'. This is only used to check whether the user has
  given a value to this parameter in L51-53. Instead, give no default value to
  inputCountData and check is the user has given input with the lines:

if (missing(inputCountData))
    countData <- getRegionCounts(inputRegions,sampleInfo,sampleDir=sampleDir,...)

tests

• [CONSIDER] Add tests using the testthat package.

[ashwathkumar]

Thanks for the feedback ! I will work on these and make a new commit soon !

[bioc-issue-bot]

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

fadd39d Changes as per 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 build report for more details.

[ashwathkumar]

Hi @dvantwisk,

I have made all the REQUIRED changes you mentioned and some of the CONSIDER one as well. I updated the package and the new build by the bot gave me the following error

"Error: package DelayedArray required by SummarizedExperiment could not be found" in OSX systems. Is this error from my side or the computer the bot ran it on? I am unsure how to go about fixing this. Any help will be appreciated.

Thanks !

[lshep]

I'm going to try and kick off a manual build of your package - DelayedArray should be available for that platform and it is odd that it is not being found.

[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.

[ashwathkumar]

I'm going to try and kick off a manual build of your package - DelayedArray should be available for that platform and it is odd that it is not being found.

Thanks a lot ! It seems there was no error in the manual build. It is odd why it wasn't able to find the package in the earlier build.

[dvantwisk]

Great! I'll have a look at your changes and get back to you soon!

[dvantwisk]

Sorry for the wait! I think the changes you made look good. I'm going to move to accept that package now.

[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!

[ashwathkumar]

Sorry for the wait! I think the changes you made look good. I'm going to move to accept that package now.

Thanks a lot @dvantwisk for taking the time to give me feedback and reviewing the package !

[mtmorgan]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/ashwathkumar.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

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

https://bioconductor.org/packages/CSSQ

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.