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(inactive) multiMiR #359

Closed mmulvahill closed 7 years ago

mmulvahill commented 7 years ago

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

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

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bioc-issue-bot commented 7 years ago

Hi @mmulvahill

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: multiMiR
Title: 
    Integration of multiple microRNA-target databases with their disease and
    drug associations
Version: 0.98.0.3
Authors@R: 
    c(person("Yuanbin", "Ru", email = "ruyuanbin@gmail.com", role = c("aut")),
      person("Matt", "Mulvahill", email = "matthew.mulvahill@ucdenver.edu", role = c("aut", "cre")),
      person("Spencer", "Mahaffey", email = "spencer.mahaffey@ucdenver.edu", role = c("aut")),
      person("Katerina", "Kechris", email = "Katerina.Kechris@ucdenver.edu", role = c("aut", "cph", "ths")))
Description: 
    A collection of microRNAs/targets from external resources, including
    validated microRNA-target databases (miRecords, miRTarBase and TarBase),
    predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm,
    miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug
    databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).
URL: https://github.com/KechrisLab/multiMiR
BugReports: https://github.com/KechrisLab/multiMiR/issues
Depends: 
    R (>= 3.3)
Imports: 
    XML, 
    RCurl, 
    purrr
Suggests: 
    BiocStyle, 
    knitr, 
    rmarkdown, 
    testthat (>= 1.0.2), 
    tibble (>= 1.2)
VignetteBuilder: knitr
License: MIT + file LICENSE
LazyData: true
NeedsCompilation: no
biocViews: miRNAData, Homo_sapiens_Data, Mus_musculus_Data,
    Rattus_norvegicus_Data, OrganismData 
RoxygenNote: 6.0.1
Encoding: UTF-8
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.

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/multiMiR_buildreport_20170505175748.html

bioc-issue-bot commented 7 years ago

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

2219fc0 Bumped to version 0.99.1 -- fixes made to resolve ...

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/multiMiR_buildreport_20170522150747.html

bioc-issue-bot commented 7 years ago

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

633711b Rebuilt documentation --

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/multiMiR_buildreport_20170522155547.html

lawremi commented 7 years ago

Obviously needs better integration with Bioconductor.

mmulvahill commented 7 years ago

A little more explanation or an example of how would be greatly appreciated.

bioc-issue-bot commented 7 years ago

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

9cf27aa Version bump (v0.99.3) -- more bioc-devel warnings...

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/multiMiR_buildreport_20170522192745.html

lawremi commented 7 years ago

We typically expect packages to plug into upstream and downstream workflows. The vignette shows many ways of retrieving miRNA annotations, etc, but does not give an example of using them in an actual analysis.

bioc-issue-bot commented 7 years ago

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

013511b wrapped more lines at 80 chars and minor restructu... 9d4594d restructed some if/else logic to minimize times sa...

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: "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/multiMiR_buildreport_20170525141422.html

bioc-issue-bot commented 7 years ago

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

6712962 Reverting sqltables changes in previous commit -- ... f560b69 Added note to README on current public release ver...

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: "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/multiMiR_buildreport_20170525155758.html

vobencha commented 7 years ago

Hi,

I've done a first review. A few suggestions and comments below.

(1) BiocCheck output:

(2) Packages in 'Imports' should be fully or partially imported in NAMESPACE.

(3) Internal functions

If you don't expect the user to call a function I would not export it. If the function is exported you need a full man page with examples. For example, add.multimir.links.Rd does not have an example.

(4) Function names:

Some have underscores, some have dots ("."). It looks like you're using dot for internal functions. If a user can call a function it technically isn't internal. I'd recommend being consistent and using underscores for all exported functions.

(5) Since this package is serving up annotations, they should support the same methods as the other annotations in Bioconductor. Please implement the select() family interface from AnnotationDbi on the objects you return from get.multimir(). The family includes select(), keys(), keytypes() and cols().

(6) Consider using the AnnotationFilter package for filtering of the results. If you feel you can't implement the filter interface in this package please explain why. The package is fairly new and if there are suggestions to expand compatibility then we'd like to hear them.

Let me know if you have questions.

Valerie

vobencha commented 7 years ago

Checking in. Are you planning to submit a new version or should I close the issue? Valerie

vobencha commented 7 years ago

Closing this issue. Please open a new issue if you decide to resubmit. Valerie

mmulvahill commented 7 years ago

@vobencha Apologies for the delay. Other work came up and didn't get notifications of your comments. I'll resubmit shortly.