philr

[jsilve24]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/jsilve24/philr

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[bioc-issue-bot]

Hi @jsilve24

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: philr
Type: Package
Title: Phylogenetic paritioning based ILR transform for metagenomics data
Version: 0.99.0
Date: August 26, 2016
Authors@R: c(person("Justin", "Silverman", role=c("aut", "cre"),
           email = "jsilve24@gmail.com"))
Author: Justin Silverman
Maintainer: Justin Silverman <jsilve24@gmail.com>
Description: PhILR is short for Phylogenetic Isometric Log-Ratio Transform.
 This package provides functions for the analysis of compositional
 data (e.g., data representing proportions of different variables/parts).
 Specifically this package allows analysis of compositional data where the parts
 can be related through a phylogenetic tree  (as is common in microbiota survey
 data) and makes available the Isometric Log Ratio transform built from the
 phylogenetic tree and utilizing a weighted reference measure.
License: GPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Imports: ape, phangorn, tidyr, ggplot2, ggtree
Depends:
Suggests: testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr
VignetteBuilder: knitr
biocViews: Sequencing, Microbiome, Metagenomics, Software
URL: https://github.com/jsilve24/philr 
BugReports: https://github.com/jsilve24/philr/issues

[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/philr_buildreport_20160901193148.html

[bioc-issue-bot]

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

e742b72 version number bump Signed-off-by: Justin Silverm...

[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/philr_buildreport_20160901202619.html

[mtmorgan]

This package seems to be in great shape with well-documented and organized code. I have only limited comments.

1. For standard licenses, e.g., GPL-3, a LICENSE.txt file is not required
2. Please clarify the role of the 'docs' folder -- this will not be installed on user systems, and seems to be extraneous to the R package?
3. Tight for loops such as at weighted_ILR.R:116 make one nervous that the code is not fully vectorized. Is that the case here, or can distp.pari be implemented as a matrix operation rather than iteration over rows & columns?

[bioc-issue-bot]

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

28f3684 changes suggested by bioconductor Thank you to mt... 023ff85 Merge branch 'hotfix/bioconductor_comments'

[jsilve24]

Regarding your points in order:

1. I removed the license file
2. docs folder currently holds the github.io site for my package (same format as the ggtree package and ggtree site, note ggtree is on bioconductor). As you mention, this folder is specified to be ignored by the .Rbuildignore file. I could also move these files to a gh-pages branch but I felt this approach was easier for me. Let me know if this is acceptable or if not I can change it.
3. Very true, thank you for catching that. the function disp.pair and distp where hold outs from earlier version of the code. I just went ahead and completely removed these functions.

Please let me know what else is needed to get philr included in the next bioconductor release.

[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/philr_buildreport_20160907140007.html