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drugTargetInteractions #1856

Closed khoran closed 3 years ago

khoran commented 3 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 3 years ago

Hi @khoran

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: drugTargetInteractions
Type: Package
Title: Drug-Target Interactions
Version: 0.99.0
Date: 2021-01-22
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke@ucr.edu>
Description: Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. 
Depends: methods, R (>= 4.0)
Imports: stats,utils, RSQLite, UniProt.ws, biomaRt,ensembldb, BiocFileCache,dplyr,rappdirs
Suggests: RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2
VignetteBuilder: knitr
License: Artistic-2.0
NeedsCompilation: no
URL: https://github.com/longevity-consortium/LC_Chemoinformatics
biocViews: Cheminformatics, BiomedicalInformatics, Pharmacogenetics, Pharmacogenomics, Proteomics, Metabolomics
RoxygenNote: 7.1.1
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: "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/drugTargetInteractions to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

khoran commented 3 years ago

The error is caused by a download timing out after 60 seconds. I'm kind of in a pickle with this. The vignette cannot have executable code without some data, but the data is too big to fit in the package. Is there any way to extend the timeout? I know another option is to create a data only package, but it's not really "generally useful" data, so it seems kind of a waste. Please let me know what would be the best way to proceed here. Thanks.

mtmorgan commented 3 years ago

Consider using BiocFileCache so that the downloads only have to 'work' occasionall http://bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#local-cache-of-an-internet-resource. Also the vignette should be illustrative rather than comprehensive so the main strategy is to use a subset of the data, perhaps stored in the package.

khoran commented 3 years ago

I am using BiocFileCache already. The resource I'm downloading doesn't seem to have the right cache headers to trigger BiocFileCache to not download it again each time. I fiddled with it for a while. I could try to subset the data. Some are id lookup tables, so it's hard to tell exactly which keys will be looked up by the code executed in the vignette. I'll see what I can do.

khoran commented 3 years ago

Upon close inspection of the error report, I've realized that the download that is timing out is not what I thought it was. This package does download a few files so I just assumed it was one of those. But the URL that is timing out is initiated by the UniProt.ws package, which I have no control over. Even if I give it just one key to query, it takes 65 seconds or so. What can I do about this?

mtmorgan commented 3 years ago

Use a cached result (i.e., saved as a small file in your package)? Find another source? the bottom line is that the build system has constraints, and your package needs to operate in them. And in general one should aim to maximize the amount of code that is actually evaluated...

khoran commented 3 years ago

submitted version 0.99.1. Several vignette chunks are using cached results now to avoid making network calls.

lshep commented 3 years ago

Please make sure to push to git.bioconductor.org to trigger a new build report. You will need to set up your remotes as described here and activate your Bioconductor credentials account as documented here

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 58d26448c9f4be03de23c3a721e2bf8d4fd96d0e

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, 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/drugTargetInteractions 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: b80018f60965ed061a56c5d9a371a8c96de46534

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/drugTargetInteractions 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: 2f8245f14e8bb2928796d1ca837f85026bbcd6a5

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: "TIMEOUT, 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/drugTargetInteractions 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: 109abecf0644aaf9ddf911bebb5db7a71d7a95e3

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/drugTargetInteractions 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: 0279dd8ff4f5cf766a628012cc147a8fb49e57ce

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

khoran commented 3 years ago

Looks like my package is passing all build tests now. Not sure if you got an automated message about that or not, so just letting you know.

Kayla-Morrell commented 3 years ago

@khoran - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

NAMESPACE

Man pages

Unit tests

R code

Best, Kayla

khoran commented 3 years ago

I have addressed all of those issues with the following exceptions/comments:

Under "R code", "clarify how objects are initialized", the object "create_time" is a data frame field identifier. It is not a variable that I can declare or a function or variable from another namespace that I can qualify. I've added a comment in the code to describe it. It is used by dplyr to sort a data frame and is resolved in the context of the dplyr::arrange function.

Regarding the last three suggestions, I've run the code through styler to fix the indents and tabs. When I run BioCheck locally though, it is still claiming there are tons of tabs and non-multiple-of-4 spaces. Upon manual inspection though, it's completely wrong. So I'm not sure what's going on there. I know there are still some lines longer than 80 chars. I'd like to leave those if possible, wrapping them just makes it less readable I think.

Kayla-Morrell commented 3 years ago

@khoran - Thank you for the explanations, your reasons are valid and can remain as is.

Kayla-Morrell commented 3 years ago

@khoran - If you have made these changes please be sure a valid version bump has been pushed to the git repo so a new build is triggered. Then I'll be able to continue with the review.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8706c6fa2cbe35ffe3671556d01139d8c6f82055

khoran commented 3 years ago

Oh, I thought I had, I think I pushed it to github but forgot upstream (bioc). Just now pushed it.

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

khoran commented 3 years ago

The build is failing on the mac with: 

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called GenomicFeatures

The package GenomicFeatures is required by ensembldb, which is required by EnsDb.Hsapiens.v86, which is declared in "suggests". Is that correct? Maybe GenomicFeatures is just not installed on the mac?

Kayla-Morrell commented 3 years ago

@khoran - Thank you for making the necessary changes. The ERROR you are experiencing on the mac builder is most likely on our side. Since the other machines are building fine I'm more than happy to accept that package.

Best, Kayla

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!

vjcitn 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/khoran.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("drugTargetInteractions"). The package 'landing page' will be created at

https://bioconductor.org/packages/drugTargetInteractions

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.