kjohnsen commented 6 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/kjohnsen/MMAPPR2

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lshep commented 5 years ago

Do you still have a data package and software package? The software package is still referencing the data package in the DESCRIPTION and the data package is still referencing the hubs in the DESCRIPTION... if any of this needs to be updated please do so asap so I know what I need to review.

bioc-issue-bot commented 5 years ago

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

4c7baf4 Modify

kjohnsen commented 5 years ago

All right. I removed the ExperimentHub BiocView in MMAPPR2data .

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lshep commented 5 years ago

A few minor things but the packages look in good shape. Nice documentation

Data Package

See notes and warnings in build report http://bioconductor.org/spb_reports/MMAPPR2data_buildreport_20190514171241.html

Software Package

Build Report

[ ] This seems like a legit and real warning that should be addressed
Checking coding practice... Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), : number of items to replace is not a multiple of replacement length Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), : number of items to replace is not a multiple of replacement length



**Vignette**
- [ ] Files/output of vignette should be written to a temporary directory and
not to the home/working directory.  Please use `tempdir()` The same should be
true for an examples in man files and tests.

bioc-issue-bot commented 5 years ago

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

b715e3b Update DESCRIPTION b1c1d6b Update MMAPPR2data.Rmd 8fa098e Update MMAPPR2data.Rmd 90de336 Update MMAPPR2data.Rmd 75acc4c Fix warnings and some notes (#3) * Update DESCRIP...

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lshep commented 5 years ago

I wanted to follow up on the changes suggested to the software package as well?

kjohnsen commented 5 years ago

I’ll have the tempdir() fix done soon, and I’ll take a look at the build warning, though it looks like it’s in the check code, not my package. Thanks again for being so patient—I’ve been working on this on top of a full-time job, so progress has been slow

kjohnsen commented 5 years ago

Looks like someone else ran into this problem last year: https://github.com/Bioconductor/Contributions/issues/749#issuecomment-390259592 I did what they Valerie suggested and changed the bash chunk to an R chunk; we'll see if that takes care of it.

bioc-issue-bot commented 5 years ago

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

7813318 Use tempdir() for output in vignette and examples a4cc966 Change bash to r chunk, add VEP installation tip 2c8d84e Bump to v0.99.8

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badf4bf Update DESCRIPTION

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a0502c1 Update docs 0fd5d68 Bump version to v0.99.19

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bioc-issue-bot commented 5 years ago

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

fa97101 Create tempOutputFolder, update docs e54256f Merge branch 'master' of https://github.com/kjohns... 722579c Bump to v0.99.10

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bioc-issue-bot commented 5 years ago

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

79135ba Update docs for tempOutputFolder f8fb313 Bump version

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kjohnsen commented 5 years ago

Hi Lori, it looks like the build is failing because a Perl module is missing the VEP needs. Is there a way we could get that installed?

lshep commented 5 years ago

I'll look into it, Thanks for pointing it out.

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lshep commented 5 years ago

The ensembl-vep error has been fixed. Please now correct the ERROR in the package code.

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

88f48fe Fix tests 56583b5 Bump version

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

7364fc0 Update tempOutputFolder doc, bump version

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kjohnsen commented 5 years ago

No errors! Are we ready? What else can I do?

lshep commented 5 years ago

For what its worth if you have specified the NAMESPACE/DESCRIPTION properly you shouldn't explicitly need to put the package name in front of the function call ie. IRanges::IRanges and Biobase::sampleNames etc... This really only needs to be done if there is a namespace conflict (where two packages have functions of the same name). But there is nothing really wrong with being explicit either; just pointing it out.
Everything else looks okay... Cheers

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lshep commented 5 years ago

@mtmorgan Please note there is a data package and a software package for addition

kjohnsen commented 5 years ago

Ok, I did the package::function thing after someone suggested it somewhere over doing imports. Might have been in Hadley Wickham's ebook.

Thanks for everything! Thanks for being so patient--it's taken a while. And thanks for insisting on testability--putting together that synthetic toy data has really made the package a lot more maintainable.

lshep commented 5 years ago

I glad you found it useful. Many are initially discouraged and find the testing/active running tedious but many also discover that it does help improve the code and makes it easier to maintain and spot bugs. Some even start developing testing before writing code to ensure robustness. We appreciate you sticking through the process. Welcome to Bioconductor!!

mtmorgan commented 5 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 (https://github.com/kjohnsen.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

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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

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(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 BiocManager::install("MMAPPR2"). 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.

mtmorgan commented 5 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 (https://github.com/kjohnsen.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 BiocManager::install("MMAPPR2data"). The package 'landing page' will be created at

https://bioconductor.org/packages/MMAPPR2data

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

(inactive) MMAPPR2 #902

Data Package

Software Package