Closed kozo2 closed 3 years ago
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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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.
@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
@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?
@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.
You did not upset me at all. Please feel free to ask questions.
Received a valid push on git.bioconductor.org; starting a build for commit id: fbe0e59fc2f828fa41f3d96fc9159e505c65021d
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.
Please check the build report carefully.
Checking package NEWS...
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.
extdata has metadata.csv
scripts - ok
ok.
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.
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 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.)
Received a valid push on git.bioconductor.org; starting a build for commit id: 38d1f7169c9c969ca16012eef56a1d1097452575
@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.
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.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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:
See further instructions 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("AHPathbankDbs")
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