drugTargetInteractions

[khoran]

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

• Repository: https://github.com/girke-lab/drugTargetInteractions Confirm the following by editing each check box to '[x]'

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

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[bioc-issue-bot]

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]

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[bioc-issue-bot]

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]

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]

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]

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]

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]

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]

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

[lshep]

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]

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

[bioc-issue-bot]

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: b80018f60965ed061a56c5d9a371a8c96de46534

[bioc-issue-bot]

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2f8245f14e8bb2928796d1ca837f85026bbcd6a5

[bioc-issue-bot]

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 109abecf0644aaf9ddf911bebb5db7a71d7a95e3

[bioc-issue-bot]

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 0279dd8ff4f5cf766a628012cc147a8fb49e57ce

[bioc-issue-bot]

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]

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]

@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

• [ ] SUGGESTION: The Description field is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph.

• [ ] REQUIRED: It looks like you utilize the 'DT' library in your vignette but you do not have the package listed as a 'Suggests'. The same goes for 'EnsDb.Hspaiens.v86'. These packages should be added to the 'Suggests' field.

• [ ] SUGGESTION: It is strongly encouraged to include the 'BugReports:' field with a relevant link to GitHub for reporting Issues.

NAMESPACE

• [ ] SUGGESTION: Generally 'importFrom()' is encouraged over importing an entire package, however if there are many functions from a single package, 'import()' is okay.

Man pages

• [ ] SUGGESTION: Use donttest{} instead of dontrun{} since donttest{} requires vaild R code. Found in the following files: getParalogs.Rd runDrugTarget_Annot_Bioassay.Rd

Unit tests

• [ ] REQUIRED: There is a 'runTests.R' file but there aren't any actual tests. This should be fixed.

R code

• [ ] REQUIRED: Clarify how 6 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). function (object) .getCacheFile (create_time) getParalogs (biomaRt) getSymEnsUp (GeneNameFilter) getSymEnsUp (values) getSymEnsUp (GeneIdFilter) getSymEnsUp (UniprotFilter)

• [ ] REQUIRED: Avoid sapply(); use vapply() if possible. Found in files: drugTargetAnnotations_Fct.R, lines 353, 365, 411, 516, 520, 522, 637, 639, 645, 647, 806, 1009, 1015, 1017, 1019

• [ ] SUGGESTION: Since you are doing some web querying for resources, you might think about adding in setting a limit on the number of times the function tries a URL. This might be helpful if the connections aren't stable all the time. Take a look at some of our documentation here, http://bioconductor.org/developers/how-to/web-query/.

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 148 lines that are > 80 characters long.

• [ ] SUGGESTION: For formatting reasons, consider 4 spaces instead of tabs. There are 183 lines that contain tabs.

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 291 lines that are not.

Best, Kayla

[khoran]

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]

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

[Kayla-Morrell]

@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]

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

[khoran]

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

[bioc-issue-bot]

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]

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]

@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]

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

Thank you for contributing to Bioconductor!

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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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

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

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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.