semisup

[rauschenberger]

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• Repository: https://github.com/rauschenberger/semisup

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[bioc-issue-bot]

Hi @rauschenberger

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: semisup
Title: Detecting SNPs with interactive effects on a quantitative trait
Description: This package implements a semi-supervised mixture model. Given partially labelled observations, it fits and tests a two-component mixture model.
Version: 0.99.0
Author: Armin Rauschenberger
Maintainer: Armin Rauschenberger <a.rauschenberger@vumc.nl>
Depends: R (>= 3.4.0)
Imports: multtest
Suggests: knitr, testthat
biocViews: SNP, GenomicVariation, SomaticMutation, Genetics, Classification, Clustering, DNASeq, Microarray, MultipleComparison
VignetteBuilder: knitr
License: GPL-3
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.

[mtmorgan]

@hpages will review this package, but I note that it makes no use of other Bioconductor packages, including standard ways of representing genomic coordinates (GRanges from the GenomicRanges package) and experimental data (SummarizedExperiment class and package). Please update your package to work with these objects, so that Bioconductor users may more easily and robustly interoperate with your package.

[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/semisup_buildreport_20170308093545.html

[bioc-issue-bot]

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

560d575 compilation problem 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, 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/semisup_buildreport_20170308121521.html

[bioc-issue-bot]

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

1a87378 problem with 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, 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/semisup_buildreport_20170308133051.html

[bioc-issue-bot]

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

54e0124 removing 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, 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/semisup_buildreport_20170308134239.html

[bioc-issue-bot]

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

98541e2 removing 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, 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/semisup_buildreport_20170308135019.html

[bioc-issue-bot]

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

bcab383 reactivate 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, 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/semisup_buildreport_20170309032505.html

[bioc-issue-bot]

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

dc09d3d vignette problem

[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/semisup_buildreport_20170309035544.html

[bioc-issue-bot]

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

975d381 travis

[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/semisup_buildreport_20170309101547.html

[bioc-issue-bot]

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

1da1356 coverage

[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/semisup_buildreport_20170309110218.html

[bioc-issue-bot]

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

425b9d1 reference manual

[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". 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/semisup_buildreport_20170310040504.html

[mtmorgan]

18 March, 2017

DESCRIPTION

• please provide a more comprehensive Description: like a paper abstract, indicating how your package provides unique functionality, and how it differs from similar offerings.

• There are no Bioconductor packages listed in the Depends / Imports / Suggests. Dependencies imply interoperability and re-use, both of which benefit end users. It seems like the GenomicRanges and SummarizedExperiment packages are relevant. Please support these packages as inputs to and outputs from your API.

NAMESPACE

• Do not export functions intended solely for internal use, e.g,. debug.mixtura

vignettes

• Good

• Do include vignette products (pdf, tex,log, out, ...) in repository.

man

• do not be too clever in introducing markup into the man pages. For instance, in the text version of the mixtura man page the argument y appears with a confusing collection of '*':

  y: *observations**:* numeric vector of length 'n'

R

• avoid 1:p when generating sequences, use seq_len(p) or seq_along(x).

• Consider using BiocParallel instead of parallel, so that Bioconductor users are exposed to a single parallel processing paradigm.

• vectorize where possible, e.g., functions.R:172

  raw <- apply(null,1,function(x) sum(x>=x[1])/perm)

  becomes

  raw <- rowSums(null > null[,1]) / perm

• avoid 'copy-and-append' functions.R:474

  trial <- list()
  for(i in 1:starts){
      trial[[i]] <-...

  in favor of pre-allocate and fill

  trial <- vector("list", starts)
  ...

  or simply use lapply() or replicate(). Since the distribution does not change during the iteration, 'hoist' this from the loop

  if (dist == "norm")
      trial <- replicate(starts, intern.norm(y,  z, it.em, epsilon))
  else ...

[bioc-issue-bot]

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

16fdd7d review

[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 following build report for more details:

http://bioconductor.org/spb_reports/semisup_buildreport_20170403102305.html

[bioc-issue-bot]

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

a4bbdcf review

[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/semisup_buildreport_20170403104715.html

[rauschenberger]

Thanks @mtmorgan for reviewing the R package semisup.

DESCRIPTION

• The description has been made more comprehensive.

• The function scrutor now accepts objects of class SummarizedExperiment.

NAMESPACE

• The internal function debug (before: debug.mixtura) has been removed from the namespace. All other internal functions have only been removed from the package index, as they might be of interest for developers.

vignettes

• All vignette products have been removed. Now the vignettes folder only contains the files semisup.Rnw and semisup.bib.

man

• The redundant asterisks have been deleted.

R

• Now the colon operator is only used in the examples. Sequence generation by 1:p has been replaced by seq_len(p) and seq_along(x).

• Parallel processing has been deactivated, because it lead to memory problems under Windows. BiocParallel will be supported at a later stage.

• Vectorisation has been used where possible.

• The function fit.wrap (before: intern.wrap) now uses lapply instead of a for loop.

[mtmorgan]

Thank you for your changes; I am happy to accept the package. It will be added to the Bioconductor svn repository and nightly builds, with additional information by email in the next several days.