switchde

[kieranrcampbell]

• Repository: https://github.com/kieranrcampbell/switchde/

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[bioc-issue-bot]

Hi @kieranrcampbell

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: switchde
Type: Package
Title: Switch-like differential expression across single-cell trajectories
Version: 0.99.0
Date: 2016-07-18
Authors@R: person("Kieran", "Campbell", email = "kieranrcampbell@gmail.com", role = c("aut", "cre"))
Description: Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.
License: GPL (>= 2)
LazyData: TRUE
biocViews: Software, Transcriptomics, GeneExpression, RNASeq, Regression, DifferentialExpression
Depends: R (>= 3.3)
Imports:
    Biobase,
    dplyr,
    ggplot2
Suggests:
    knitr,
    rmarkdown,
    BiocStyle,
    testthat,
    numDeriv
VignetteBuilder: knitr
RoxygenNote: 5.0.1
URL: https://github.com/kieranrcampbell/switchde
BugReports: https://github.com/kieranrcampbell/switchde

[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/switchde_buildreport_20160718124149.html

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

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

64f8d87 Increment version num

[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/switchde_buildreport_20160718153906.html

[bioc-issue-bot]

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

aeb2b9b added monocle and hsmmsinglecell to suggests

[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/switchde_buildreport_20160718154815.html

[bioc-issue-bot]

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

bbb3e45 Updated bundled data to have more genes; removed m...

[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/switchde_buildreport_20160719084246.html

[bioc-issue-bot]

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

9255803 Forgot to add new data to repo

[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, 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/switchde_buildreport_20160719085109.html

[bioc-issue-bot]

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

151b6af Added man files for synthetic data; removed random...

[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/switchde_buildreport_20160719085945.html

[bioc-issue-bot]

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

e3d3565 Removed pval testing too - doesn't work on windows

[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/switchde_buildreport_20160719090859.html

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

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

b7d0247 Complete rewrite of model fitting to be cleaner an...

[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/switchde_buildreport_20160721104950.html

[bioc-issue-bot]

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

ade3596 Minor bug fix

[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/switchde_buildreport_20160721122746.html

[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/switchde_buildreport_20160725090708.html

[lshep]

Hello, I have reviewed your package and have a few comments to address:

NAMESPACE:

1. you shouldn't need importFrom(dplyr,filter) when you already import the entire dplyr package with import(dplyr)
2. Please consider adding the imports and imports from suggested in the package build report to remove the "no visible global function definition" notes: Consider adding importFrom("methods", "is") importFrom("stats", "coef", "dnorm", "lm", "median", "optim", "p.adjust", "pchisq", "var") importFrom("Biobase", pData") importFrom("numDeriv", "grad")
3. We would appreciate if you could also correct the package build report notes on "no visible binding for global variable". See ?globalVariables

R CODE: You shouldn't need "::" when calling functions from the package "dplyr" as it should be imported from the specification in the namespace.

VIGNETTE:

1. If the directories switchde_vignette_cache and switchde_vignette_files are not necessary please remove.
2. Please add a section utilizing Bioconductor object. According to the man page, it seems like these functions can utilize a SCESet of scater but there is no example. Please add in this example to the vignette in a separate section.
3. Add an installation section including:

source("https://bioconductor.org/biocLite.R")
biocLite("switchde")

MAN If sanitise_inputs and sigmoid can be run by user, please provide an example.

README Should also contain the instructions for installing using biocLite() as demonstrated above in addition to the devtools method.

Thank you Lori

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

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

40e5d82 Sorted scater import, bumped version number

[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/switchde_buildreport_20160725173008.html

[kieranrcampbell]

Hello,

Thanks very much for your help and feedback. I think I've addressed all the above issues with the exception of the following:

importFrom("numDeriv", "grad")

Since grad is only used in the test_that functions then library(numDeriv) there should be sufficient?

Please add a section utilizing Bioconductor object.

This has been added but inline with the current example, since except for the initial function call switchde(...) the rest of the examples would be identical.

If sanitise_inputs and sigmoid can be run by user, please provide an example.

These are meant for internal use only but documented using roxygen2 for consistency.

Thanks

Kieran

[lshep]

Thank you for clarification. Could you add @keyword internal to the man pages for sanitise_inputs and sigmoid

[bioc-issue-bot]

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

335a920 Added keyword internal to santise_inputs and sigmo...

[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/switchde_buildreport_20160726102551.html

[kieranrcampbell]

Could you add @keyword internal to the man pages for sanitise_inputs and sigmoid

This has been fixed in the latest commit.

[lshep]

Thank you for making these changes. The package looks okay now and I will recommend be accepted. You should get svn instructions via email in the next couple of days.

[kieranrcampbell]

Thanks very much.

Kieran

[kieranrcampbell]

Hello,

I still haven't received any email, just wondering if I should have?

Kieran

[lshep]

Sorry for the delay. It is in the list to get sent out, you should get it soon.