Bioconductor / Contributions

Contribute Packages to Bioconductor
135 stars 33 forks source link

excluderanges #2269

Closed mdozmorov closed 3 years ago

mdozmorov commented 3 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]'

I am familiar with the essential aspects of Bioconductor software management, including:

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 3 years ago

Hi @mdozmorov

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: excluderanges
Title: Genomic coordinates of problematic genomic regions
Version: 0.99.1
Authors@R: c(
    person(given = "Mikhail",
 family = "Dozmorov",
 role = c("aut", "cre"),
 email = "mikhail.dozmorov@gmail.com",
 comment = c(ORCID = "0000-0002-0086-8358")),
    person(given = "Eric",
 family = "Davis",
 role = c("aut")),
    person(given = "Wancen",
 family = "Mu",
 role = c("aut")),
    person(given = "Stuart",
 family = "Lee",
 role = c("aut")),
    person(given = "Tim",
 family = "Triche",
 role = c("aut")),
    person(given = "Douglas",
 family = "Phanstiel",
 role = c("aut")),
    person(given = "Michael",
 family = "Love",
 role = c("aut"))
 )
Description: Genomic coordinates of problematic genomic regions that should be
    avoided when working with genomic data. GRanges of exclusion 
    regions (formerly known as blacklisted), centromeres, telomeres, known 
    heterochromatin regions, etc. (UCSC 'gap' table data). Primarily for human 
    and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies. 
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
URL: https://github.com/mdozmorov/excluderanges
BugReports: https://github.com/mdozmorov/excluderanges/issues
Suggests: 
    BiocStyle,
    knitr,
    RefManageR,
    rmarkdown,
    rCGH,
    sessioninfo,
    AnnotationHub
VignetteBuilder: knitr
biocViews: AnnotationData, AnnotationHub, FunctionalAnnotation, GenomicSequence
bioc-issue-bot commented 3 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.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 3 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: "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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/excluderanges to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mdozmorov commented 3 years ago

Does the "Warnings" label prevent the review? From previous experience, it wasn't a problem, but I want to make sure it's not the reason for the delay.

lshep commented 3 years ago

No it should not prevent review @vjcitn

vjcitn commented 3 years ago

Can I ask why there are csv files in /man in this package?

mdozmorov commented 3 years ago

Some may prefer links to the source files, per @mikelove's suggestion. These tables were originally embedded in Markdown. I can keep csv files only on GitHub, and embed the tables for BioC submission.

vjcitn commented 3 years ago

It seems to me that if you want to provide CSV data, you could put it in inst/extdata or inst/csv. I have a feeling this selection of /man as the location has a somewhat involved history -- but I don't know of any other examples of putting csv data in /man. I see images in /man and I have a recollection that this is a workaround for getting images into the github README. I don't think the same practice should be used for small csv data, but I could be persuaded otherwise.

mdozmorov commented 3 years ago

The CSV files are now in inst/extdata. It indeed seems the right place for them, according to https://r-pkgs.org/data.html.

vjcitn commented 3 years ago

did you push revisions and bump version number to

origin  https://git.bioconductor.org/packages/excluderanges (fetch)
origin  https://git.bioconductor.org/packages/excluderanges (push)
mdozmorov commented 3 years ago

I double-checked - I cannot push to https://git.bioconductor.org/packages/excluderanges. The error is:

fatal: remote error: FATAL: W any packages/excluderanges nobody DENIED by fallthru (or you mis-spelled the reponame)

I also tried git@git.bioconductor.org:packages/excluderanges.git, and also rejected

! [remote rejected] main -> main (hook declined) error: failed to push some refs to @.***: packages/excluderanges.git'

The changes are in the original repository, including version bump https://github.com/mdozmorov/excluderanges

mikelove commented 3 years ago

I think this is because GitHub main / Bioc master. Try this:

git push upstream main:master

this is from the comment in step 5 here: https://bioconductor.org/developers/how-to/git/new-package-workflow/

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4a32389a5e5a197bbac953ccf86e21995ea9344c

mdozmorov commented 3 years ago

Worked like a charm! Didn't know one can match branch names. Thanks, @mikelove

bioc-issue-bot commented 3 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: "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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/excluderanges to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

vjcitn commented 3 years ago

Very nice vignette. But are the download operations in eval=FALSE going to be replaced with Hub operations? I think we are ready to accept, but BiocCheck complains that too few vignette chunks are evaluated.

mdozmorov commented 3 years ago

Yes, after the files will be added to AHub, I'll update the vignette and the readme to use AHub IDs. Download links will be gone.

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

vjcitn commented 3 years ago

Please do make the changes to use hub resources before this is accepted.

mdozmorov commented 3 years ago

Sent the e-mail to hubs@bioconductor.org, and will make changes asap.

lshep commented 3 years ago

Please check your metadata.csv file and the files you have uploaded. I had everything added to the hub and since removed as in testing some of the file names are not matching up. For instance the very first entry the RDataPath excluderanges/ce10.Kundaje.ce10-blacklist.rds does not match any file uploaded, I assume this is the uploaded excluderanges/ce10.Kundaje.ce10-Excludable.rds -- I'm not sure how many other of these mistakes there are but please check and either update the metadata.csv file or reupload the entire data set with the correct names to S3 (the same access credentials will be good)

mdozmorov commented 3 years ago

I'm sorry for the oversight, strange. I re-generated the data from scratch and ensured the file names match entries in the metadata table. Just uploaded the updated data with all file names matched.

image

lshep commented 3 years ago

The RDataPath field has still not been updated. As pointed out before this is the problematic field and still is.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 780e17b84c756c7bd0870b6fba055e4e672daebf

mdozmorov commented 3 years ago

Should be updated. Lots of renaming has been done, I forgot about the RDataPath field in metadata.

bioc-issue-bot commented 3 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: "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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/excluderanges to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 3 years ago

The data has been added to the hub

> ah = AnnotationHub()
snapshotDate(): 2021-10-08

> query(ah, "excluderanges")
AnnotationHub with 42 records
# snapshotDate(): 2021-10-08
# $dataprovider: UCSC, ENCODE, mitra.stanford.edu/kundaje/akundaje/release/b...
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabdi...
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH95908"]]' 

            title                                                    
  AH95908 | ce10.Kundaje.ce10-Excludable.rds                         
  AH95909 | dm3.Kundaje.dm3-Excludable.rds                           
  AH95910 | hg19.Bernstein.Mint_Excludable_hg19.rds                  
  AH95911 | hg19.Birney.wgEncodeDacMapabilityConsensusExcludable.rds 
  AH95912 | hg19.Crawford.wgEncodeDukeMapabilityRegionsExcludable.rds
  ...       ...                                                      
  AH95945 | mm10.UCSC.telomere.rds                                   
  AH95946 | mm9.UCSC.centromere.rds                                  
  AH95947 | mm9.UCSC.contig.rds                                      
  AH95948 | mm9.UCSC.fragment.rds                                    
  AH95949 | mm10.UCSC.scaffold.rds         

> temp = ah[["AH95908"]]
 GRanges object with 122 ranges and 0 metadata columns:
        seqnames            ranges strand
           <Rle>         <IRanges>  <Rle>
    [1]     chrI     933000-934500      *
    [2]     chrI   2542900-2544000      *
    [3]     chrI   3171400-3172600      *
    [4]     chrI   3664800-3666100      *
    [5]     chrI   3989700-3991000      *
    ...      ...               ...    ...
  [118]     chrX 14388000-14389200      *
  [119]     chrX 14907900-14909700      *
  [120]     chrX 15226900-15228800      *
  [121]     chrX 15807400-15811200      *
  [122]     chrX 16758300-16760000      *
  -------
  seqinfo: 6 sequences from ce10 genome

Please update the vignettes accordingly Cheers

vjcitn commented 3 years ago

Vignette should not have:

BiocManager::install("mdozmorov/excluderanges")

And should revise

## Use excluderanges

{r eval = FALSE}
# hg38 excluderanges coordinates
download.file(url = "https://drive.google.com/uc?export=download&id=1Jy_7cvFj5ZHUUwHgGUKZeFk8lFCalpKk", destfile = "hg38.Kundaje.GRCh38_unified_Excludable.rds")

etc

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6922d18b964be4af828aea2e9a9ea462f05adffb

mdozmorov commented 3 years ago

I realized I didn't push the update to BioC, only to GitHub. This push uses all AHub data, no download.file etc., and BioCcheck() returns zero warnings.

bioc-issue-bot commented 3 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: "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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/excluderanges to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 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: "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 build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/excluderanges to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

vjcitn commented 3 years ago

If you can figure out the warning, please fix -- and let me know how you figured it out. Seems like an immature warning condition in R CMD check.

lshep commented 3 years ago

The warning is because there are no man pages whatsoever so there are no files to parse. We would recommend having at least a package level man page to describe the package and point to any relevant functions so something like ?excluderanges would work for a user

vjcitn commented 3 years ago

I suspected this. Can BiocCheck introduce a clearer response to this condition? A package with no man pages at all should be exceptional if allowed at all. @LiNk-NY ...

lshep commented 3 years ago

This came from R CMD check not BiocCheck -- so you would still get he cryptic error unless fixed in base R

mdozmorov commented 3 years ago

It may help to check for such cases in BioCcheck and explicitly suggest adding package documentation. I couldn't understand the problem from R CMD check output. Pushed the documentation, will monitor if it resolves the warning.

lshep commented 3 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/mdozmorov.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

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

https://bioconductor.org/packages/excluderanges

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.