csawBook - Githubissues

LTLA commented 4 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/LTLA/csawBook

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bioc-issue-bot commented 4 years ago

Hi @LTLA

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: csawBook
Version: 0.99.0
Date: 2020-10-07
Title: The Book of csaw 
Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email =
    "infinite.monkeys.with.keyboards@gmail.com")
Depends: csaw,
    chipseqDBData,
    edgeR,
    TxDb.Mmusculus.UCSC.mm10.knownGene,
    org.Mm.eg.db,
    rtracklayer,
    Rsamtools,
    Gviz,
    knitr,
    BiocStyle
biocViews: Workflow, EpigeneticsWorkflow
Description: 
    Describes how to use the csaw package to detect differentially bound regions in ChIP-seq data. 
    This provides instructions on how to read in BAM files to obtain a per-window count matrix, 
    filtering to obtain high-abundance windows of interest, 
    normalization of sample-specific biases, testing for differential binding, 
    consolidation of per-window results to obtain per-region statistics,
    and annotation and visualization of the DB results.
License: GPL-3
VignetteBuilder: knitr
BiocType: Book

LTLA commented 4 years ago

All content here was migrated from csawUsersGuide, which I hope this will replace. I also plan to migrate the content in chipseqDB into this book, thus enabling consolidation of all csaw-related documentation into a single location.

hpages commented 4 years ago

I wonder why the SPB didn't kick in. Anyways, this can go directly to the main builds.

Looks good. Please suggest rebook and add BiocType: Book to the DESCRIPTION.

Thanks

hpages commented 4 years ago

I just got this after trying to build the book locally on my laptop (got the error after 2h26m):

...
...
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Quitting from lines 117-122 (index.Rmd) 
Error in fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) : 
  statmod package required but is not installed
Calls: local ... glmQLFit -> glmQLFit.default -> squeezeVar -> fitFDistRobustly

Execution halted

So it looks like statmod also needs to go to Depends or Suggests (using Depends indeed seems to make more sense for books). Thx

LTLA commented 4 years ago

I think this needs to go into the "under review" category or something to trigger creation of the repo on the BioC git server.

hpages commented 4 years ago

ok let's see what happens

LTLA commented 4 years ago

Hmm. Do you see a csawBook repository on your side?

hpages commented 4 years ago

Gosh, that thing took 7h to build on my laptop!

hpages@spectre:~$ time bdevbuild csawBook
* checking for file ‘csawBook/DESCRIPTION’ ... OK
* preparing ‘csawBook’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* creating default NAMESPACE file
* building ‘csawBook_0.99.0.tar.gz’

real    418m49.024s
user    49m15.256s
sys 9m42.879s

Hmm. Do you see a csawBook repository on your side?

Nope:

hpages@spectre:~/sandbox$ git clone https://git.bioconductor.org/packages/csawBook
Cloning into 'csawBook'...
fatal: remote error: FATAL: R any packages/csawBook nobody DENIED by fallthru
(or you mis-spelled the reponame)

Lori @lshep, Martin @mtmorgan, or Nitesh @nturaga, any idea?

Thx

lshep commented 4 years ago

@hpages --- it was awaiting moderation for @mtmorgan to do an initial look and add to git through the api and interface -- please don't manually change -- we will add to git and let you know when it can proceed

LTLA commented 4 years ago

@hpages Funny, it takes less than an hour to build on my laptop. Might depend on how much EHub data it needs to pull down.

bioc-issue-bot commented 4 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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hpages commented 4 years ago

Might depend on how much EHub data it needs to pull down.

I hope that's it. We have crappy internet here in Seattle, the home town of Amazon, which is ironical. 20 years ago we had fast and high quality internet in Europe for a 3rd of the price we're paying here.

hpages commented 4 years ago

Indeed. 2nd time is much better:

hpages@spectre:~$ time bdevbuild csawBook
* checking for file ‘csawBook/DESCRIPTION’ ... OK
* preparing ‘csawBook’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* creating default NAMESPACE file
* building ‘csawBook_0.99.0.tar.gz’

real    48m58.256s
user    45m39.890s
sys 1m19.977s

No need to replace my laptop yet.

hpages commented 4 years ago

Not sure what the SPB is up to but there's no need to wait.

bioc-issue-bot commented 4 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

mtmorgan commented 4 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/LTLA.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("csawBook"). The package 'landing page' will be created at

https://bioconductor.org/packages/csawBook

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

csawBook #1758