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AHPathbankDbs #1825

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kozo2 opened this issue Dec 18, 2020 · 18 comments
Closed
9 tasks done

AHPathbankDbs #1825

kozo2 opened this issue Dec 18, 2020 · 18 comments
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@kozo2
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@kozo2 kozo2 commented Dec 18, 2020

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 understand that by submitting my package to Bioconductor,
    the package source and all review commentary are visible to the
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    instructions. My package is consistent with the Bioconductor
    Package Guidelines.

  • I understand that a minimum requirement for package acceptance
    is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS.
    Passing these checks does not result in automatic acceptance. The
    package will then undergo a formal review and recommendations for
    acceptance regarding other Bioconductor standards will be addressed.

  • My package addresses statistical or bioinformatic issues related
    to the analysis and comprehension of high throughput genomic data.

  • I am committed to the long-term maintenance of my package. This
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@bioc-issue-bot bioc-issue-bot commented Dec 18, 2020

Hi @kozo2

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: AHPathbankDbs
Type: Package
Title: Metabolites and proteins linked to PathBank pathways (for AnnotationHub)
Version: 0.99.1
Encoding: UTF-8
Authors@R:
    person(given = "Kozo",
 family = "Nishida",
 role = c("aut", "cre"),
 email = "kozo.nishida@gmail.com",
 comment = c(ORCID = "0000-0001-8501-7319"))
Depends: R (>= 4.1.0)
Imports: AnnotationHub (>= 2.23.0)
Suggests: BiocStyle,
    magrittr,
    dplyr,
    tibble,
    knitr
Description: The package provides a comprehensive mapping table of 
    metabolites and proteins linked to PathBank pathways, including
    HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for
    each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus",
    "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus",
    "Caenorhabditis elegans", "Rattus norvegicus",
    "Drosophila melanogaster", and "Pseudomonas aeruginosa").
    These table information can be used for Metabolite Set Enrichment Analysis.
VignetteBuilder: knitr
License: Open Database License
URL: https://github.com/biopackathon/AHPathbankDbs
LazyData: true
RoxygenNote: 7.0.2
biocViews: AnnotationHub, CustomDBSchema, FunctionalAnnotation

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@bioc-issue-bot bioc-issue-bot commented Dec 19, 2020

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

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@bioc-issue-bot bioc-issue-bot commented Dec 19, 2020

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/AHPathbankDbs to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@kozo2
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@kozo2 kozo2 commented Dec 20, 2020

@nturaga I can't fetch the upstream. (So I can't trigger new build report...) What do you think?
(I fixed the "WARNINGS" on the origin. But I can't push the update to upstream.)

> cat ~\.ssh\id_ed25519.pub
ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIFT4ynvtxZT5assytXlFBMqTYy8Jl1Pnkcs0cSbY94Zm
> git remote -v
origin  git@github.com:biopackathon/AHPathbankDbs.git (fetch)
origin  git@github.com:biopackathon/AHPathbankDbs.git (push)
upstream        git@git.bioconductor.org:packages/AHPathbankDbs.git (fetch)
upstream        git@git.bioconductor.org:packages/AHPathbankDbs.git (push)
(base) PS C:\Users\kozon\Projects\AHPathbankDbs> git fetch --all
Fetching origin
Fetching upstream
git@git.bioconductor.org: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

@kozo2
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@kozo2 kozo2 commented Dec 22, 2020

@nturaga I think this is because I changed the contents of https://github.com/kozo2.keys after creating this issue. Could you please check the SSH public key registration again?

@kozo2
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@kozo2 kozo2 commented Dec 23, 2020

@nturaga I'm sorry for upsetting you. I understand the reason.
The reason was that the Bioconductor Git Credentials and the GitHub Credentials were out of sync.
(and I did not know how the Bioconductor Git Credentials works ).
Now the git fech -all works well.

@nturaga
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@nturaga nturaga commented Dec 23, 2020

You did not upset me at all. Please feel free to ask questions.

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@bioc-issue-bot bioc-issue-bot commented Dec 25, 2020

Received a valid push on git.bioconductor.org; starting a build for commit id: fbe0e59fc2f828fa41f3d96fc9159e505c65021d

@bioc-issue-bot
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@bioc-issue-bot bioc-issue-bot commented Dec 25, 2020

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

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/AHPathbankDbs to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@nturaga
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@nturaga nturaga commented Jan 8, 2021

Review

General

Please check the build report carefully.

Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.

DESCRIPTION

    • NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph
  • It looks like an Annotationhub package, did you contact @lshep or
    @Kayla-Morrell already? This doesn't look like anything is needed in
    AWS S3, it's pulling from Pathbank.

NAMESPACE

  • ok

inst

  • extdata has metadata.csv

  • scripts - ok

vignettes

ok.

@lshep
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@lshep lshep commented Jan 8, 2021

The data is already in AnnotationHub and the data is already in Bioconductor S3 bucket. If it is pulling the data from some other place the code should be updated to use the AnnotationHub front end. But since the vignette is clearly already referencing AnnotationHub it should be good.

@nturaga
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@nturaga nturaga commented Jan 8, 2021

I see, ok so it seems Kozo downloads CSV metadata from Pathbank for the databases which are already in AnnotationHub in our S3 bucket.

Can you confirm @kozo2 ?

@kozo2
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@kozo2 kozo2 commented Jan 8, 2021

I see, ok so it seems Kozo downloads CSV metadata from Pathbank for the databases which are already in AnnotationHub in our S3 bucket.

Can you confirm @kozo2 ?

I confirmed it with the code below. (I also added this code to AHPathbankDbs vignette.)

> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2021-01-04
> ah
AnnotationHub with 55009 records
# snapshotDate(): 2021-01-04
# $dataprovider: Ensembl, BroadInstitute, UCSC, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Haemcode, FungiDB, Inparanoid8, TriTrypDB, PlasmoDB, MicrosporidiaDB
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Bos taurus, Rattus norvegicus, Pan troglodytes, Danio rerio, Gallus gallus, Monodelphis domestica, Felis catus
# $rdataclass: GRanges, TwoBitFile, BigWigFile, EnsDb, Rle, OrgDb, ChainFile, TxDb, Inparanoid8Db, data.frame
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH5012"]]' 

            title                                       
  AH5012  | Chromosome Band                             
  AH5013  | STS Markers                                 
  AH5014  | FISH Clones                                 
  AH5015  | Recomb Rate                                 
  AH5016  | ENCODE Pilot                                
  ...       ...                                         
  AH89321 | Ensembl 102 EnsDb for Xiphophorus couchianus
  AH89322 | Ensembl 102 EnsDb for Xiphophorus maculatus 
  AH89323 | Ensembl 102 EnsDb for Xenopus tropicalis    
  AH89324 | Ensembl 102 EnsDb for Zonotrichia albicollis
  AH89325 | Ensembl 102 EnsDb for Zalophus californianus

> mcols(query(ah, "pathbank"))

I paste the image to check the metadata.
(Because it didn't render well in markdown.)

image

@bioc-issue-bot
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@bioc-issue-bot bioc-issue-bot commented Jan 8, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 38d1f7169c9c969ca16012eef56a1d1097452575

@kozo2
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@kozo2 kozo2 commented Jan 9, 2021

@nturaga

Checking package NEWS...

  • NOTE: Consider adding a NEWS file, so your package news will be
    included in Bioconductor release announcements.

Fixed

DESCRIPTION

    • NOTE: The Description field in the DESCRIPTION is made up by less
      than 3 sentences. Please consider expanding this field, and
      structure it as a full paragraph

Fixed

  • It looks like an Annotationhub package, did you contact @lshep or
    @Kayla-Morrell already? This doesn't look like anything is needed in
    AWS S3, it's pulling from Pathbank.

Yes. I contacted @lshep and @Kayla-Morrell already.
I uploaded the rda files to S3 last month. (I think I did NOT upload the metadata.csv to S3.)
It's pulling data from S3. Not from Pathbank.

inst

  • extdata has metadata.csv

extdata has metadata.csv, but I think the metadata in the above code is not from this extdata but from S3.

@bioc-issue-bot
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@bioc-issue-bot bioc-issue-bot commented Jan 9, 2021

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

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/AHPathbankDbs to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

@bioc-issue-bot
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@bioc-issue-bot bioc-issue-bot commented Feb 11, 2021

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

Thank you for contributing to Bioconductor!

@mtmorgan
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@mtmorgan mtmorgan commented Feb 11, 2021

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/kozo2.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("AHPathbankDbs"). The package 'landing page' will be created at

https://bioconductor.org/packages/AHPathbankDbs

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.

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