Closed mdozmorov closed 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
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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.
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.
No it should not prevent review @vjcitn
Can I ask why there are csv files in /man in this package?
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.
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.
The CSV files are now in inst/extdata. It indeed seems the right place for them, according to https://r-pkgs.org/data.html.
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)
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
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/
Received a valid push on git.bioconductor.org; starting a build for commit id: 4a32389a5e5a197bbac953ccf86e21995ea9344c
Worked like a charm! Didn't know one can match branch names. Thanks, @mikelove
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.
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.
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.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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Please do make the changes to use hub resources before this is accepted.
Sent the e-mail to hubs@bioconductor.org, and will make changes asap.
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)
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.
The RDataPath field has still not been updated. As pointed out before this is the problematic field and still is.
Received a valid push on git.bioconductor.org; starting a build for commit id: 780e17b84c756c7bd0870b6fba055e4e672daebf
Should be updated. Lots of renaming has been done, I forgot about the RDataPath field in metadata.
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.
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
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
Received a valid push on git.bioconductor.org; starting a build for commit id: 6922d18b964be4af828aea2e9a9ea462f05adffb
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.
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.
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.
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.
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.
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
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 ...
This came from R CMD check
not BiocCheck -- so you would still get he cryptic error unless fixed in base R
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.
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