Hi @ChristopherEeles

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: CoreGx
Type: Package
Title: Classes and Functions to Serve as the Basis for Other 'Gx' Packages
Version: 0.2.0
Date: 2020-03-22
Authors@R: c(
    person("Petr","Smirnov", email = "petr.smirnov@uhnresearch.ca", role = c("aut")),
    person("Ian","Smith", email = "ianc.smith@mail.utoronto.ca", role = c("aut")),
    person("Christopher", "Eeles", , email = "christopher.eeles@uhnresearch.ca", role = c("aut")),
    person("Benjamin", "Haibe-Kains",  email = "benjamin.haibe.kains@utoronto.ca", role = c("aut", "cre"))
    )
Description: A collection of functions and classes which serve as the foundation 
    for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This 
    package was created to abstract shared functionality from other lab package 
    releases to increase ease of maintainability and reduce code repetition in 
    current and future 'Gx' suite programs. Major features include a 'CoreSet' 
    class, from which 'RadioSet' and 'PharmaSet' are derived, along with get and 
    set methods for each respective slot. Additional functions related to 
    fitting and plotting dose response curves, quantifying statistical 
    correlation and calculating area under the curve (AUC) or survival fraction
    (SF) are included. For more details please see the included documentation, 
    as well as: 
    Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., 
      Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., 
      Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>.
    Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M.,
      Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
VignetteBuilder: knitr
VignetteEngine: knitr::rmarkdown
biocViews: Software, Pharmacogenomics, Classification, Survival
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: 
    Biobase,
    S4Vectors,
    SummarizedExperiment,
    piano, 
    parallel, 
    methods, 
    stats, 
    utils, 
    graphics, 
    grDevices, 
    lsa, 
    testthat
Suggests: pander, 
  rmarkdown,
  knitr
License: GPL-3
RoxygenNote: 7.1.0

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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: "skipped, 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.

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Received a valid push; starting a build. Commits are:

804475d BiocSubmission: Version number to 0.99.0; added ...

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: "ABNORMAL".
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.

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: "ABNORMAL".
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.

Received a valid push; starting a build. Commits are:

97ea3a9 BiocSub: Version bump to 0.99.1 to trigger rebui...

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: "ABNORMAL".
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.

Received a valid push; starting a build. Commits are:

e63565d BiocSub: Revert dependency to R >= 4.0; fixing d...

Received a valid push; starting a build. Commits are:

7d824dd BiocSub: 1 hr no build report? Retriggering build ...

Hi @nturaga,

I am not receiving build reports for my recent commits. Also bioc-issue-bot is making two comments per commit.

Could be a problem with bioc-issue-bot?

Please advise.

Are you bumping the version number each time?

@nturaga

Are you bumping the version number each time?

Yes. I even did an arbitray bump to retrigger the build on your servers. I get the 'valid push; starting build' comment and email, but no build report is ever posted.

Try to reenable your hook

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: "skipped, 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.

@nturaga

^ CoreGx rebuild with no errors or warnings

NEWS: I was able to parse the news file after installing the package using utils::news(); please let me know if this is not what you meant

R:

• CoreSet: updated constructor to use new accessor functions instead of @; also corrected in other parts of the package
• Connectivity Score: removed the "gsea' argument and added an error to notify users of the parameter change
• mclapply: Swapped in bplapply as per request
• CATASTROPHIC FAILURE: removed this comment and the commented out code
• .mcc: Rewrote the function to be cleaner; generally plan to improve coding style over the coming months
• Removed testthat usage from utitlites

vignette:

• Switched to BiocStyle

Received a valid push; starting a build. Commits are:

aa902fd Add: New branch plus version bump
5fc8209 Update: Resolving Bioc review feedback
4ddbc39 Update: Package building after Bioc updates; runni...
22f425c Fix: Passing BiocChecks without errors/warnings
fef1044 Update: Addressed Bioc reviewer comments
3b361a4 Update: Passing BiocCheck with only notes"

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.

@nturaga

^ RadioGx passing with no warnings or errors

NEWS: I updated the news file to display without warnings, but for some reason, it didn't make it through my merge; I will update it to the working version on the next push

R:

• RadioSet: I updated the constructor to be in line with CoreGx and reviewer comments
• Accessors: I wrote a number of new accessor methods to ensure we aren't using @ to get data from our slots
  • the generics for these are currently defined in RadioGx, but will be moved to CoreGx for the next push (after next round of feedback)
  • In utilities.R there are some accesses using @ due to the fact that we are comparing an older version of the RadioSet class with the new one; we have already removed accessor methods for the old version
    • The purpose of the .validateRsetMolecu... function is to ensure that no information was lost from our curated objects as we transition from ExpressionSets to SummarizedExperiemnts; this function will be removed in future releases.
• mclapply: Swapped in bplapply as per request
• Commented out code: I believe I have removed all commented out code and hope it improves readability
• Coding style: I realize that some of our functions are hard to read, we are in the process of refactoring all four packages (CoreGx, PharmacoGx, RadioGx, ToxicoGx) and plan to get the codebase in shape within a month or two. Until then please let me know if there are any style issues I should address immediately
• formatR: I ran it over our codebase for RadioGx but it broke some stuff and in general seemed to decrease readability. As we refactor our code we plan to ensure all variables and functions have descriptive names; we also intend to factor our large functions into manageable units but it will take some time
• Removed testthat usage from utitlites
• matrixStats: I changed the apply statements to use rowMeans/Medians and colMeans/Medians as per request; there are also some sapply's I couldn't change to vapply because the return type is not clear - this will be addressed the upcoming refactor

vignette:

• Switched to BiocStyle
• In terms of updating the vignette we agree that a detailed vignette is needed and will attempt to put this together in the next month

Received a valid push; starting a build. Commits are:

3755de9 Add: Development branch while Bioconductor submiss...
354afde Add: as(SummarizedExperiment, "ExpressionSet") Fo...
b98108c Fix: sinseTo never removed "DMSO" from drugMatr... [cbb208d](https://github.com/bhklab/ToxicoGx/commit/cbb208d6cd4c6c0b5bc7e453689a1fddf800507a) Fix: subsetTonever removed "DMSO" fromdrugMat...
be9ab16 Merge pull request #2 from bhklab/master Change u...
82f6c85 Merge branch 'development' of github.com:bhklab/To...
8977df2 Merge branch 'development'
f7d11db Update: Version bump for Bioc release; changed som...
3790487 Updated utilites.R to use new accessor methods; ...
e40efe2 Fix: Resolved weird NAMESPACE errors from roxygen... [ec86a75](https://github.com/bhklab/ToxicoGx/commit/ec86a75f451191d345ae884edc1d62f3fefe6574) Fix: Resolved weird NAMESPACE errors from roxygen...
b65953a Update: Passing BiocCheck() with only NOTES
1e2159d Merge: development into master to trigger Bioc...

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.

Received a valid push; starting a build. Commits are:

7153a4e Fix: Version bump to trigger rebuild

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.

Received a valid push; starting a build. Commits are:

ce8c33f Fix: Converted accesses of tSet to use accessors
e0175ae Update: Fix incorrect parameter name in accessor c...
34110f4 Merge branch 'development'
d9f1eb9 Update: Version bump for Bioc rebuild

@nturaga

Our current Bioconductor package PharmacoGx has significant updates that depend on CoreGx. Since we removed it from CRAN for this submission, we are unable to update the package until CoreGx is available on Bioconductor.

Given it is the last day for package acceptance is there any chance to expedite acceptance of CoreGx? We put a lot of effort into the PharmacoGx changes and would very much like them to be available in this release.

If it means resubmitting RadioGx and ToxicoGx separately that is acceptable.

Thanks either way.

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.

@nturaga

Our current Bioconductor package PharmacoGx has significant updates that depend on CoreGx. Since we removed it from CRAN for this submission, we are unable to update the package until CoreGx is available on Bioconductor.

Given it is the last day for package acceptance is there any chance to expedite acceptance of CoreGx? We put a lot of effort into the PharmacoGx changes and would very much like them to be available in this release.

If it means resubmitting RadioGx and ToxicoGx separately that is acceptable.

Thanks either way.

Hi, Let's do that. Let's get the review of CoreGx in and keep ToxicoGx and RadioGx seperate. That way, you can meet your urgency for the PharmacoGx package.

I'll only review CoreGx now.

Hi, Let's do that. Let's get the review of CoreGx in and keep ToxicoGx and RadioGx seperate. That way, you can meet your urgency for the PharmacoGx package.

I'll only review CoreGx now.

I really appreciate it. Should we resubmit ToxicoGx/RadioGx as separate issues or will we just continue here later?

Hi, Let's do that. Let's get the review of CoreGx in and keep ToxicoGx and RadioGx seperate. That way, you can meet your urgency for the PharmacoGx package.
I'll only review CoreGx now.

I really appreciate it. Should we resubmit ToxicoGx/RadioGx as separate issues or will we just continue here later?

Just delete the comments which add ToxicoGx and RadioGx as additional packages. And submit them as seperate issues.

I'll review CoreGx and try to get it to you as soon as possible.

Hi @ChristopherEeles ,

I'm ok accepting the package for now since there is a time crunch. I have to point out a few things and insist you do them.

1. Improve the vignette. The fact that you are just pointing people to 3 other packages, doesn't really help them. Especially if they are all them are related. Try to improve it just enough so that they have a sense of how CoreGx helps the other 3 packages.

2. Write test cases, because this package lays a foundation for your other packages. Failure here could trickle down into other packages.

Please make these improvements ASAP.

Your package has been accepted. It will be added to the
Bioconductor Git repository and nightly builds. Additional
information will be posed to this issue in the next several
days.

Thank you for contributing to Bioconductor!

Hi @ChristopherEeles ,

I'm ok accepting the package for now since there is a time crunch. I have to point out a few things and insist you do them.

1. Improve the vignette. The fact that you are just pointing people to 3 other packages, doesn't really help them. Especially if they are all them are related. Try to improve it just enough so that they have a sense of how CoreGx helps the other 3 packages.

2. Write test cases, because this package lays a foundation for your other packages. Failure here could trickle down into other packages.

Please make these improvements ASAP.

Thanks, Nitesh! I will improve the vignette by the end of next week. As for unit tests, we already have a bunch written that we can migrate from PharmacoGx. Our goal will be to hit 90% coverage for all three packages before the next Bioconductor release.

How long until CoreGx will be available as a dependency? Will it be today or tomorrow?

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

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