apeglm - Githubissues

azhu513 commented 7 years ago

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

Repository: https://github.com/azhu513/apeglm

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 7 years ago

Hi @azhu513

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: apeglm
Title: Approximate posterior estimation for GLM coefficients
Version: 0.0.10
Authors@R: c(person("Anqi Zhu", "Developer", role = c("aut", "cre"), email = "anqizhu@live.unc.edu"),
   person("Joseph G. Ibrahim", "Developer", role = "aut", email = "jibrahim@email.unc.edu"),
   person("Michael I. Love", "Developer", role = "aut", email = "michaelisaiahlove@gmail.com"))
Description: apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
VignetteBuilder: knitr
Imports: emdbook, stats, utils
Suggests: BiocStyle, airway, knitr
License: GPL (>=2)
Encoding: UTF-8
LazyData: true
biocViews: Sequencing, RNASeq, DifferentialExpression, GeneExpression
RoxygenNote: 6.0.1

bioc-issue-bot commented 7 years ago

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 commented 7 years ago

Carefully consider how your package can interoperate more effectively with Bioconductor packages, in particular through re-use of common classes for input and (possibly) output.

bioc-issue-bot commented 7 years ago

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/apeglm_buildreport_20170807191532.html

mikelove commented 7 years ago

@mtmorgan we expect the functions here will mostly be run as a routine within a DESeq2 function.

Still, we can easily change so apeglm works with SummarizedExperiment input with counts as assay and then output a GRanges (the primary output of the main function is log fold changes). Would that be better?

mtmorgan commented 7 years ago

yes, better to work with SE and output GRanges. Thanks!

bioc-issue-bot commented 7 years ago

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

cddc501 Update with RSE and SE, update version number

bioc-issue-bot commented 7 years ago

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/apeglm_buildreport_20170809105839.html

azhu513 commented 7 years ago

Hi, When I run BiocCheck locally I didn't have this error. I have subscribed to the bioc-devel mailing list as well. Can I know how to fix it then please?

dvantwisk commented 7 years ago

I am not seeing the maintainer's email, anqizhu@live.unc.edu, on the list of mailing list subscribers. The mailing list should have sent you an email asking you to verify your subscription, did you confirm your subscription with this email?

azhu513 commented 7 years ago

I just found this confirmation email in my spam folder. Just confirmed.

dvantwisk commented 7 years ago

You're in! Just try doing another push to confirm that everything builds correctly.

bioc-issue-bot commented 7 years ago

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

74d1176 update maintainer email address

bioc-issue-bot commented 7 years ago

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/apeglm_buildreport_20170809121321.html

dvantwisk commented 7 years ago

Great! We'll start reviewing your package now!

dvantwisk commented 7 years ago

We've reviewed your package! It looks great, but there are a few issues we would like you to address. Please address these issues and respond back to us when you are ready for us to continue the review.

DESCRIPTION:

[CONSIDER] LICENSE: specify a specific GPL license version.

NAMESPACE:

Looks fine!

R/apelgm.R

L65: [CONSIDER] Create lightweight S4 object for output to apeglm() with accessors instead of outputting a list of matrices.
L140: [CONSIDER] Consider using match.arg() to improve style of function declaration. For example, the parameter interval.type can have three values: "laplace", "HPD", or "credible". The parameter in the function declaration can be written as interval.type=c('laplace', 'HPD', 'credible'). The value that the chooser uses can be obtained with interval.type <- match.arg(interval.type). The first value (in this case 'laplace') is the default argument. Using this method makes it clear to users what the allowed inputs to a function are and may also make error catching easier.

R/bbEstDisp.R

Looks fine!

R/grid.R

L342-350, L363-371: [CONSIDER] These two for-loops are essentially the same. Consider making a function and invoking it in these two locations instead of repeating blocks of code.

R/logLikes.R

Looks fine!

R/priorVar.R

Looks fine!

R/svalue.R

L27: [CONSIDER] use seq_along() here.

test

[CONSIDER] add tests to your package using the testthat package.

vignettes

Looks fine!

bioc-issue-bot commented 7 years ago

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

a943e8a Add match.arg for interval types; revise grid.R an... a7cf80e license version GPL-2

bioc-issue-bot commented 7 years ago

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/apeglm_buildreport_20170821125055.html

azhu513 commented 7 years ago

Hi Daniel, Just wondering if everything is ok with the package? Should we do something now? Thanks!

dvantwisk commented 7 years ago

Hi,

We were just waiting for you to finish your changes. I assume you have addressed the issues we put forward in our review, so we can have another look at your package now. Is this correct?

azhu513 commented 7 years ago

Yes, we addressed all except the we did not create an S4 class output for the package, as this package will be called via DESeq2's lfcShrink function which has it's own input and output classes. Thus we prefer to just have list output of the apeglm() function.

dvantwisk commented 7 years ago

Hello, We've reviewed the package again. The only remaining issue is that the tests that you added in the tests/testthat directory do not actually contain any tests. Tests contain the key functions expect_*() (for example, expect_true() would be a test). After adding tests, they can be run with devtools::test() in your package's directory. Here is a resource on writing testthat tests: https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf

bioc-issue-bot commented 7 years ago

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

9886ca6 add more in testthat

bioc-issue-bot commented 7 years ago

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/apeglm_buildreport_20170911205238.html

azhu513 commented 7 years ago

hi @dvantwisk, we have added tests, can you please review?

dvantwisk commented 7 years ago

Everything looks good now!

bioc-issue-bot commented 7 years ago

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!

azhu513 commented 7 years ago

Hi, Just wondering if this is hosted on Bioconductor yet? I never got the information about the Bioconductor git repo. I'd like to make a change, should i just push to my Github repo please?

mtmorgan commented 7 years ago

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 (tithub.com/.keys is not empty), then no further steps are required. Otherwise, do the following:

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

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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.

Bioconductor / Contributions

apeglm #446