methyvim

[nhejazi]

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• Repository: https://github.com/nhejazi/methyvimData

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[bioc-issue-bot]

Hi @nhejazi

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: methyvimData
Title: Example experimental data for use with the methyvim package
Version: 0.9.0
Authors@R: person("Nima", "Hejazi", email = "nhejazi@berkeley.edu",
        role = c("aut", "cre"))
Description: Contains a reduced set of simulated data inspired by data produced
   by the Infinium EPIC BeadChip assays by Illumina. The example data
   set is made available to highlight many of the key procedures that
   are available within the core functions of the methyvim package.
Depends: R (>= 3.4.0)
Suggests: Biobase, SummarizedExperiment, minfi
License: file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1

[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: "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/methyvimData_buildreport_20170829163700.html

[bioc-issue-bot]

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

b42211a fix bioc errors

[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".
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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/methyvimData_buildreport_20170829164631.html

[bioc-issue-bot]

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

e0b0154 further fix bioc errors

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvimData_buildreport_20170829165525.html

[bioc-issue-bot]

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

db48bf3 add vignettebuilder

[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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http://bioconductor.org/spb_reports/methyvimData_buildreport_20170829171652.html

[bioc-issue-bot]

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

0b52bba fix vignette, version bump

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvimData_buildreport_20170829173256.html

[nhejazi]

AdditionalPackage: https://github.com/nhejazi/methyvim

[bioc-issue-bot]

Dear @nhejazi ,

You (or someone) has already posted that repository to our tracker.

See #463

You cannot post the same repository more than once.

[nhejazi]

@mtmorgan @vobencha -- It seems that the repo corresponding to the analysis package is already being tracked by the issue for the first submission attempt (though #463 is now closed). What is the best way to continue with the submission process?

[bioc-issue-bot]

Hi @nhejazi,

Starting build on additional package https://github.com/nhejazi/methyvim.

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

The DESCRIPTION file of this additional package is:

Package: methyvim
Title: Differential Methylation Analysis with Targeted Minimum Loss-Based
  Estimates of Variable Importance Measures
Version: 0.2.5
Authors@R: c(
  person("Nima", "Hejazi", email = "nhejazi@berkeley.edu",
role = c("aut", "cre", "cph")),
  person("Rachael", "Phillips", email = "rachaelvphillips@berkeley.edu",
role = "ctb"),
  person("Alan", "Hubbard", email = "hubbard@berkeley.edu", role = "ctb"),
  person("Mark", "van der Laan", email = "laan@stat.berkeley.edu",
role = "aut")
  )
Author: Nima Hejazi [aut, cre, cph], Rachael Phillips [ctb], Alan Hubbard [ctb],
  Mark van der Laan [aut]
Maintainer: Nima Hejazi <nhejazi@berkeley.edu>
Description: This package provides facilities for differential methylation
  analysis based on variable importance measures (VIMs), a class of statistical
  target parameters that arise in causal inference. The estimation and inference
  procedures provided are nonparametric, relying on ensemble machine learning to
  flexibly assess functional relationship among covariates and the outcome of
  interest. These tools can be applied to differential methylation at the level
  of CpG sites, with valid inference after multiple hypothesis testing.
Depends:
  R (>= 3.4.0)
License: file LICENSE
URL: https://github.com/nhejazi/methyvim
BugReports: https://github.com/nhejazi/methyvim/issues
Encoding: UTF-8
LazyData: true
Imports:
  stats,
  methods,
  ggplot2,
  gridExtra,
  superheat,
  wesanderson,
  magrittr,
  dplyr,
  gtools,
  tmle,
  future,
  doFuture,
  BiocParallel,
  BiocGenerics,
  SummarizedExperiment,
  GenomeInfoDb,
  bumphunter,
  IRanges,
  limma,
  minfi
Suggests:
  testthat,
  knitr,
  rmarkdown,
  BiocStyle,
  SuperLearner,
  randomForest,
  earth,
  gam
VignetteBuilder: knitr
RoxygenNote: 6.0.1
biocViews:
  Clustering,
  DNAMethylation,
  DifferentialMethylation,
  MethylationArray,
  MethylSeq

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvim_buildreport_20170829180109.html

[bioc-issue-bot]

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

0ef6641 bump version to match Bioc initial submission

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvim_buildreport_20170829210604.html

[vobencha]

Please address this issue raised by the single package builder:

• Checking exported objects have runnable examples...
  • ERROR: At least 80% of man pages documenting exported objects
    must have runnable examples. The following pages do not:
    fdr_msa.Rd, methytmle-class.Rd, methyvim.Rd

Once the package passes with no errors I'll do a full review.
Valerie

[bioc-issue-bot]

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

44ce674 bump version -> bioc rebuild

[vobencha]

I will review the package today.
Valerie

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvim_buildreport_20171002131536.html

[bioc-issue-bot]

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

5dd1823 loosen test tolerance for windows builds

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvim_buildreport_20171002135151.html

[nhejazi]

Thanks very much, Valerie -- looking forward to your review. At this point, I've worked out all errors and warnings from the builds. The lingering error is something that I cannot quite pin down on the tokay1 machine. It might be something obvious to you, but I'm missing it.

[vobencha]

Hi,

• Data Package

  • Nice man page. Please add a small example showing how to load the data and manipulate.
  • Remove LazyData: true

• Software Package

  • Remove LazyData: true
  • All man pages need running examples or explain why you think you can't provide one.
  • Vignette is well written with good examples.

Valerie

[bioc-issue-bot]

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

2be0a83 rm lazydata=true option
9b27f27 add working example
aad1dbf bump version for bioc rebuild
b507616 Merge pull request #1 from nhejazi/bioc-review re...

[nhejazi]

Hi Valerie ---

Thanks very much for your review. I have made nearly all of the requested changes in the most recent PRs to the methyvimData and methyvim repos. In particular each of the following have been addressed:

• Data Package: methyvimData

  • Please add a small example showing how to load the data and manipulate.
  • Remove LazyData: true

• Software Package: methyvim

  • Remove LazyData: true
  • All man pages need running examples or explain why you think you can't provide one.

In particular, with respect to the functions missing runnable examples -- those being limma_screen, methyvim_tmle, cluster_sites, set_parallel, and force_positivity -- these are all helper functions internally used by the main user-facing methyvim function or other helper functions that it calls. These intentionally lack examples (and are not marked with an @export tag) because users are discouraged from directly calling these functions. I fear that including examples might encourage their use outside of their intended use-cases. That being said, all of these functions do have included unit tests that are clearly organized within the tests/testthat subdirectory -- the potential contributor could consult these in order to ensure they understand these functions. I hope this clears up any remaining concerns with regard to the status of the package. Please let me know if I can provide more information.

Best,
Nima

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvimData_buildreport_20171003004746.html

[bioc-issue-bot]

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

948c814 rm lazydata=true
04e2713 revisions to man pages
c017c51 bump version
d30d5af Merge pull request #26 from nhejazi/bioc-review r...

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvim_buildreport_20171003142342.html

[vobencha]

Hi Nima,
If those functions are just used internally then you probably don't need a man page. Is there a reason why you feel you need one?

If you feel strongly about keeping the man pages I would mark them as 'Internal Use Only' and be clear about the use / intent.
Valerie

[nhejazi]

Hi Valerie ---

I just figured having man pages would be nice in case potential contributors want to refer to them eventually. I can just revert the documentation for these functions from Roxygen to regular comments if that's the recommended best practice currently.

My personal preference would be the second option --- I'm happy to add a disclaimer to the man pages of each of those functions, something along the lines of "Internal Use Only: this function is not meant to be user-facing". (My thinking was that most users will have a hard enough time using them since they'll need the ::: operator, given that these functions are not exported anyway.)

Please let me know which of these you prefer and I'll implement it today. Since this is the last outstanding item for the review, I'm hoping to have the package marked as accepted for Bioc3.6 this week, if that's at all possible.

Best,
Nima

[vobencha]

Yes, keeping the man pages and marking them as 'Internal' sounds good.
Valerie

[vobencha]

Did you implement the change in the man pages? Once that's done I can go ahead and approve the package.

[bioc-issue-bot]

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

08927c8 note un-exported functions; use @Keywords to suppr...
0e28673 rebuild docs
575f425 add initial pkgdown materials
b262913 add pkgdown index
14285d3 bump version => 0.99.8
2c0d31c Merge pull request #27 from nhejazi/biocdocs Impr...

[nhejazi]

Thanks for checking in. As of the latest build, I've added the text "INTERNAL USE ONLY" to the main description for each of those functions; moreover, I've also marked them with @keywords internal in their Roxygen documentation, so as to suppress the functions appearing in the manual and index but still preserve their help pages. This seemed like a good compromise of what we had discussed.

[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 following build report for more details:

http://bioconductor.org/spb_reports/methyvim_buildreport_20171005000027.html

[vobencha]

Looks good. Thanks for making the changes - package is approved.
Valerie

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor Git repository and nightly builds. Additional
information will be sent to the maintainer email address in
the next several days.

Thank you for contributing to Bioconductor!

[nhejazi]

Great to hear. @vobencha -- thanks very much for the review!

[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/nhejazi.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

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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 biocLite(\"methyvimData\"). The package 'landing page' will be created at

https://bioconductor.org/packages/methyvimData

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.

[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/nhejazi.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 biocLite(\"methyvim\"). The package 'landing page' will be created at

https://bioconductor.org/packages/methyvim

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.