yduan004 commented 3 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/yduan004/customCMPdb

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 3 years ago

Hi @yduan004

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: customCMPdb
Title: Customize and Query Compound Annotation Database
Description: This package serves as a query interface for important community collections of
    small molecules, while also allowing users to include custom compound collections. 
Version: 0.99.0
Authors@R: 
    c(person("Yuzhu", "Duan", role = c("aut", "cre"),
 email = "yduan004@ucr.edu",
 comment = c(ORCID = "YOUR-ORCID-ID")),
      person("Thomas", "Girke", email = "thomas.girke@ucr.edu", 
 role = "aut"))
Depends: R (>= 4.0)
Imports: AnnotationHub, RSQLite, XML, utils, ChemmineR, gdata, methods, stats
Suggests: knitr, rmarkdown, testthat, BiocStyle
License: Artistic-2.0
biocViews: Software, Cheminformatics
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/yduan004/customCMPdb/
BugReports: https://github.com/yduan004/customCMPdb/issues
RoxygenNote: 7.1.1
NeedsCompilation: no

bioc-issue-bot commented 3 years ago

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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: "ERROR". 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/customCMPdb 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

Received a valid push on git.bioconductor.org; starting a build for commit id: bb4c595abeb4526ec69c0dee4cf07cf487f002be

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: "ERROR, skipped". 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/customCMPdb 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

Received a valid push on git.bioconductor.org; starting a build for commit id: 23cc806f4b9c75e45b1ccbd35bc556750ecdb1e6

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: "ERROR". 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/customCMPdb 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

Received a valid push on git.bioconductor.org; starting a build for commit id: 64af9bf01f6aa2e218f90925eff6c5095a5e3c81

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: "ERROR". 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/customCMPdb 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

Received a valid push on git.bioconductor.org; starting a build for commit id: 79405684e2bbab68ce616b27edb23352ad905986

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.

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/customCMPdb 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

Thank you for your submission to Bioconductor. Please see the initial review below:

general

[ ] Was this package meant to import data into the hubs? It looks like you have the inst/scripts and inst/extadata/metadata.csv file but nothing has been added to the hubs? It looks like maybe this information moved to a different package compoundCollectionData?
[ ] It looks like you have an accompanied package that the data was moved into compoundCollectionData. This package should be officially submitted to Bioconductor for review as stated when the package data was originally submitted to the hubs in the email on 3/31/2020. Since this appears to be the accompanied data pacakge for this software package I would suggest submitting under this issue as a related package. The package compoundcollectiondata must have a formal review and be submitted to bioconductor or the data will be removed from the hub.

vignette

[ ] remove customCMPdb.html. Vignettes should be interactively built.

R

drugage_annot.R

processDrugage:

[ ] We generally discourage random downloads. This should either be stored in the hubs or minimally the file should be cached so that if it is ever not available for download users may used a cached version.
[ ] You hard coded downloads directory to unzip. The user should control where the file is downloaded to.
[ ] Hard coded paths seem to suggest this function would be broken for other users chembldb <- "/bigdata/girkelab/shared/lcshared/chemoinformatics/compoundDBs/chembl_24/chembl_24_sqlite/chembl_24.db"

downloadUniChem:

[ ] Same comments as above. Minimally files should be cached and the user should be allowed to specify a write directory.

manageCMAP.R

[ ] Same as above getDmap should not download and save information to a users home directory without asking users permission or allowing user to specify output directory. And download files should be minimally cached.
[ ] change print to message

Please submit the accompanied package as soon as possible and implement the changes recommended above. When ready please perform a version bump to trigger a new build and comment here on what has been updated and that you are ready for a re-review. Cheers

yduan004 commented 3 years ago

Hi Lori, @lshep

Thanks for reviewing my package. The situation is that I previously planned to write two packages, one software and one data package, where the data package used to store the compound annotation and structure databases, and the software package used as query and customization interface. The data package is named as compoundCollectionData and the data has been uploaded to AnnotationHub on 3/31/2020. The software package is named as customCompoundDB. But with the consideration that the data is of small size and overall this is a small utility package, it is unnecessary to have two packages. So I decided to merge the two packages into one package to simplify maintainability. So customCMPdb is a combination of the both the data and software packages, it contains the descriptions of the data that are already submitted to AnnotationHub.

So my specific question is whether it will be possible to rename the accompanied compoundCollectionData package as customCMPdb? This way, the package submitted to AnnotationHub will be customCMPdb, and is being reviewed. I hope this solution can be accepted. If it is accepted, I will editing the metadata in the customCMPdb package accordingly. I will respond to your R comments later. Looking forward to your response.

Best, Yuzhu

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 203be8f606f2cd0088b05be3bc047d6f0a4a1a69

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.

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/customCMPdb 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

Received a valid push on git.bioconductor.org; starting a build for commit id: f9d9fbee8a2433d312ce8aab45d5e99530321ccb

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.

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

yduan004 commented 3 years ago

Hi Lori, @lshep

Thanks for reviewing my package. Here are my further responses to your comments.

general

[x] Was this package meant to import data into the hubs? It looks like you have the inst/scripts and inst/extadata/metadata.csv file but nothing has been added to the hubs? It looks like maybe this information moved to a different package compoundCollectionData?
[x] It looks like you have an accompanied package that the data was moved into compoundCollectionData. This package should be officially submitted to Bioconductor for review as stated when the package data was originally submitted to the hubs in the email on 3/31/2020. Since this appears to be the accompanied data package for this software package I would suggest submitting under this issue as a related package. The package compoundcollectiondata must have a formal review and be submitted to bioconductor or the data will be removed from the hub.

YD response: I have responded to this issue in my last post, please take a look at it. I hope the suggestion/request of renaming the compoundCollectionData package as customCMPdb could be accepted. In addition, in the metadata.csv file, I have changed all compoundCollectionData to customCMPdb. I have also made changes all over the package. Now the customCMPdb is the only one package that is a combination of both data and software packages. The datasets have been uploaded to AnnotationHub previously.

vignette

[x] remove customCMPdb.html. Vignettes should be interactively built.

The html file of the vignette has been removed.

R

_drugageannot.R

processDrugage:

[x] We generally discourage random downloads. This should either be stored in the hubs or minimally the file should be cached so that if it is ever not available for download users may used a cached version.

Thanks for this very helpful comment! I have addressed this issue by using utilities in the BiocFileCache package to download online resources to user’s cache directory by using bfc <- BiocFileCache(cache=rappdirs::user_cache_dir(appname="customCMPdb"), ask=TRUE) code.

[x] You hard coded downloads directory to unzip. The user should control where the file is downloaded to.

Now, all the downloads are stored in user’s cache directory. The ‘tar.gz’ files are also extracted under the cache directory for future uses, it is only done once.

[x] Hard coded paths seem to suggest this function would be broken for other users chembldb <- "/bigdata/girkelab/shared/lcshared/chemoinformatics/compoundDBs/chembl_24/chembl_24_sqlite/chembl_24.db"

Sorry, it was an oversight on my part to include this hard coded path in my package. Thanks for pointing this out! Now, this hard coded path has been deleted. Instead the corresponding data are downloaded from the corresponding ftp site of ChEMBL and stored under cache.

downloadUniChem:

[x] Same comments as above. Minimally files should be cached and the user should be allowed to specify a write directory.

This function has been deleted. Now the downloaded files are all cached, and the path of the output files are specified by users.

manageCMAP.R

[x] Same as above getDmap should not download and save information to a users home directory without asking users permission or allowing user to specify output directory. And download files should be minimally cached.

The getDmap function has been deleted, and the DMap dataset is now included in the extdata directory of the customCMPdb package.

[x] change print to message

The print has been deleted since it is not necessary. Now, the message function is used all over the R scripts for places where outputting a message to users. Thanks for pointing out.

The package is ready for your re-review. Thanks again for your time!

Best, Yuzhu

lshep commented 3 years ago

In the future, We generally still recommend separating experiment or annotation packages no matter how light weight to have a clear distinction between data and software. Also in general, if hub data does not have an associated package it would be removed (this happen to just slip through the cracks for the CompoundCollectData to still be available). But if you wish to proceed with one package, I can take care of the renaming. For What Its Worth, this isn't a simple task and will involve extra time on my end not only to rename directories on S3 but also to manually manipulate entries in our database for each of your files. When I'm finished with the renaming, I'll do a re-review of the updated package.

lshep commented 3 years ago

The data in the hub has been updated to be associated with this package

> ah = AnnotationHub()
snapshotDate(): 2020-10-14
> query(ah, "customCMPdb")
AnnotationHub with 5 records
# snapshotDate(): 2020-10-14
# $dataprovider: Broad Institute, DrugBank, DrugAge, DrugBank, Broad Institu...
# $species: Homo sapiens
# $rdataclass: character
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH79563"]]' 

            title         
  AH79563 | annot_0.1     
  AH79564 | drugage_build2
  AH79565 | drugbank_5.1.5
  AH79566 | cmap02        
  AH79567 | lincs_pilot1

Please make sure everything still works as expect. Then please do another version bump so we can ensure the resources are still accessible in the package on the builders as well.

yduan004 commented 3 years ago

Hi Lori, @lshep

Thank you very much for renaming things. I am sorry for making additional work on your end... I will make a version bump right away to ensure everything still works. Thanks again for your help!

Best, Yuzhu

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ddf4223b7d8819aaed853f5e4b0d2ced82e8fb3a

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.

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

yduan004 commented 3 years ago

Hi Lori @lshep, the check status is OK, please re-review the package. Many thanks!

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!

yduan004 commented 3 years ago

Hi Lori, thanks for reviewing and accepting the package!

mtmorgan 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/yduan004.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("customCMPdb"). The package 'landing page' will be created at

https://bioconductor.org/packages/customCMPdb

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

customCMPdb #1680

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R

general

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