Xeva : XEnograft Visualization & Analysis

gangeshberi commented 5 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/bhklab/Xeva

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bioc-issue-bot commented 5 years ago

Hi @gangeshberiuhn

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: Xeva
Type: Package
Title: Analysis of patient-derived xenograft (PDX) data
Version: 0.99.5
Author: Arvind Mer, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Description: Contains set of functions to perform analysis of patient-derived xenograft (PDX) data.
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 6.1.1
LazyData: true
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown
Imports:
  methods,
  stats,
  utils,
  BBmisc,
  Biobase,
  grDevices,
  ggplot2,
  ComplexHeatmap,
  foreach,
  parallel,
  doParallel,
  doSNOW,
  Rmisc,
  grid
Depends: R (>= 3.5)
biocViews: GeneExpression, Pharmacogenetics, Pharmacogenomics, Software, Classification
BugReports: https://github.com/bhklab/Xeva/issues

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bioc-issue-bot commented 5 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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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.

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bioc-issue-bot commented 5 years ago

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

d22f7a3 changed R verion

bioc-issue-bot commented 5 years ago

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

d22f7a3 changed R verion

bioc-issue-bot commented 5 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: "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.

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bioc-issue-bot commented 5 years ago

Dear Package contributor,

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bioc-issue-bot commented 5 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.

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spocks commented 5 years ago

@lshep we have the same issue again! For 1st build we had only one warning WARNING: Update R version dependency from 3.5 to 3.6 . I fixed this but now it says build results were: "ABNORMAL" . Also there are 2 commits.

gangeshberi commented 5 years ago

It seems the webhook has been triggered once but there are 2 commits.

bioc-issue-bot commented 5 years ago

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

834b170 version 0.99.7

bioc-issue-bot commented 5 years ago

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

834b170 version 0.99.7

bioc-issue-bot commented 5 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: "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.

Please see the build report for more details.

bioc-issue-bot commented 5 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: "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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bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

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bioc-issue-bot commented 5 years ago

Dear Package contributor,

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bioc-issue-bot commented 5 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

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lshep commented 5 years ago

I still don't know why this is occurring and I am very sorry for the inconvenience this is causing. I'll take over review of this package and can manually kick off builds so you can get an accurate report.

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

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spocks commented 5 years ago

Hi @lshep : thank you for helping us out with package building. Please let us know if any more changes required before acceptance. The associated manuscript of the package in under revision and it requires bioconductor acceptance of the package. We will be very grateful if package can be accepted on bioconductor in coming weeks. Thanks again for your help!

lshep commented 5 years ago

Again I apologzie for this inconvenience and we apologize for being at a loss for what is going on with the webhooks and build reports.

Since there is still the issue with multiple builds occurring on a valid version bump I would actually advise removing the webhook and requesting a manually build to avoid the noise. Just tag me and I'll try to kick one off quickly - If you don't mind the noise you can keep the webhook active and I'll try to hop on to kick off a build when I see it going crazy.

General

[ ] from the build report please fix the coding practices NOTES of using vapply instead of sapply and seq_len() or seq_along() instead of 1:...
[ ] We strongly encourage the use of unit tests to test correctness and accuracy of code
[ ] Why include the dontrun in the getExperiment? The exampels run instaneously
[ ] Similarly why the dontrun in setResponse it seems to run fairly efficiently.

NEWS

[ ] Please remove the ============ at the bottom of the file.

NAMESPACE

[ ] There are a lot of exports please ensure that all of these should be exposed to the user and that some of these should not be internal and only called within other functions

DESCRIPTION

[ ] Please remove LazyData: true in our experience this rarely proves useful and can often slow down installation of the package.

README

[ ] please also include Bioconductor install instructions

Vignette

[ ] I suggest changing the name of the vignette to the name of the package. While this is entirely optional its is much more intuitive for a user to do vignette("Xeva") than try to hunt down the name of the vignette to do vignette("getting-started")
[ ] Its fine that you start with an object to use for the example in the vignette but considering the object is a specialized class you have created at least reference the functions that the user can look at to create their own.

MAN

[ ] braca.Rd please include source information and more detail for this dataset.
[ ] ALL man documents could use more detail. When looking at the documentation when investigating the dontruns, I can't figure out what most of the arugments are in setResponse and getExperiment especially ones where you just indicate default used. There should be explaintation of what these arguments are and how they are used; if they are not used then they should be removed. This applies to all man files/functions
[ ] Please include an example for your class constructor - I currently have no idea how to create an object of the class to be able to use in the vignette pipeline since you provided the object already in your class format.

R code General

[ ] We recommend the use of BiocParallel over parallel. Please explain if not going to update
[ ] ExpressionSets are outdated and have been replaced with SummarizedExperiments. Please update all instances unless you can provide very good reasoning for not.
[ ] Remove commented out code. This should be added only when live

XevaSet_Class.R

[ ] I have no idea how to create an object of your class

access_expressionData_functions.R

[ ] expressionsets are outdated. update to use a summarizedExperiment
[ ] we don't encourage half implemented code - remove .batch2DataFram and batch_SummarizedMolProfiles and include only when code is live. (you should be able to git track this)

access_slot_drug.R

[ ] Should there be any sort of validation for the replacement/setting of drugInfo slot? Does the data.frame need a particular format?

access_slot_expDesign.R

[ ] remove commented out code until live
[ ] What about the case that both are not null?
[ ] What happens in getBatchFormatted, when in the else? can all values still be the default NULL or should something be defined?

access_slot_experiment.R

[ ] (optional) seems like the print method for the object class should be with the class definition in XevaSet_Class.R.

checkModel.R

[ ] Again optional but perhaps this is better placed with the XevaSet_Class.R code.

creat_Experiment_slot.R

[ ] modelClassS4Vars() where did these hard coded values come from?

create_drug_slot.R

[ ] could this function be combined with a different file to reduce the number of different files? What is the point of this function?

create_modToBiobaseMap_slot.R/create_sensitivity_slot.R

[ ] Again completely optional but if these are validity methods (which it seems like) then it is probably best to include in the file that has the class definiation.

Going to stop here but apply those general concepts above throughout. Please ping when you are ready for a review and include a summary of the changes or comment on any questions placed above. I can kick off a manual build when you are ready for review again to ensure the most accurate build report.

Cheers and I look forward to working with you to getting the package accepted to Bioconductor.

bioc-issue-bot commented 5 years ago

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

960b234 version bump

spocks commented 5 years ago

Hi @lshep, thanks for your detailed comments. We have address all the comments and have made substantial changes in the code. The only thing that we can’t change at this moment is switch to SummarizedExperiments. As I have explained later also this is due to dependency on PharmacoGx package. We are working on the new release of PharmacoGx package where we plan to switch to SummarizedExperiments for both the packages. Please find our response to the issues below. We are looking forward to be accepted to Bioconductor.

General

[x] from the build report please fix the coding practices NOTES of using vapply instead of sapply and seq_len() or seq_along() instead of 1:...

We have replaced all sapply and 1:...
[x] We strongly encourage the use of unit tests to test correctness and accuracy of code

We have performed unit tests for some important functions. In future we plan to update it for all necessary functions and will release it on github.
[x] Why include the dontrun in the getExperiment? The exampels run instaneously

We have fixed this issue.
[x] Similarly why the dontrun in setResponse it seems to run fairly efficiently.

We have removed the dontrun from the function.

NEWS

[x] Please remove the ============ at the bottom of the file.

We have fixed this issue.

NAMESPACE

[x] There are a lot of exports please ensure that all of these should be exposed to the user and that some of these should not be internal and only called within other functions

We have made sure that only the required functions are exported. We have also removed several functions from the export.

DESCRIPTION

[x] Please remove LazyData: true in our experience this rarely proves useful and can often slow down installation of the package.

We have fixed this issue.

README

[x] please also include Bioconductor install instructions

We have fixed this issue.

Vignette

[x] I suggest changing the name of the vignette to the name of the package. While this is entirely optional its is much more intuitive for a user to do vignette("Xeva") than try to hunt down the name of the vignette to do vignette("getting-started")

We have fixed this issue.
[x] Its fine that you start with an object to use for the example in the vignette but considering the object is a specialized class you have created at least reference the functions that the user can look at to create their own.

In the vignette, we have included a section to create object with an example and required data is also included.

MAN

[x] braca.Rd please include source information and more detail for this dataset.

We have fixed this issue.
[x] ALL man documents could use more detail. When looking at the documentation when investigating the dontruns, I can't figure out what most of the arugments are in setResponse and getExperiment especially ones where you just indicate default used. There should be explaintation of what these arguments are and how they are used; if they are not used then they should be removed. This applies to all man files/functions

Fixed. We have rechecked all the man documents to make sure all arguments are described.
[x] Please include an example for your class constructor - I currently have no idea how to create an object of the class to be able to use in the vignette pipeline since you provided the object already in your class format.

We have included a detailed example in the vignette.

R code General

[x] We recommend the use of BiocParallel over parallel. Please explain if not going to update
[x] ExpressionSets are outdated and have been replaced with SummarizedExperiments. Please update all instances unless you can provide very good reasoning for not.

For both of these issues, at the moment it is not possible to switch. This is because of the dependency on another Bioconductor package from our group, PharmacoGx. We are working on the new version of PharmacoGx, where we plan to implement these changes in both Xeva and PharmacoGx.
[x] Remove commented out code. This should be added only when live

We have fixed this issue.

XevaSet_Class.R

[x] I have no idea how to create an object of your class

We have included an example in the function documentation. Furthermore a detailed example is also included in the Vignette under the section “Creating new Xeva object”.

access_expressionData_functions.R

[x] expressionsets are outdated. update to use a summarizedExperiment

This is because of the dependency on another Bioconductor package from our group, PharmacoGx. We are working on the new version of PharmacoGx, where we plan to implement these changes in both Xeva and PharmacoGx.
[x] we don't encourage half implemented code - remove .batch2DataFram and batch_SummarizedMolProfiles and include only when code is live. (you should be able to git track this)

We have reviewed the code and made sure no part of the code is half implemented.

access_slot_drug.R

[x] Should there be any sort of validation for the replacement/setting of drugInfo slot? Does the data.frame need a particular format?

We have fixed this issue.

access_slot_expDesign.R

[x] remove commented out code until live

We have fixed this issue.
[x] What about the case that both are not null?

In such case batch will take precedent. Have included it in the details.
[x] What happens in getBatchFormatted, when in the else? can all values still be the default NULL or should something be defined?

Fixed in code. Now in such case it returns error.

access_slot_experiment.R

[x] (optional) seems like the print method for the object class should be with the class definition in XevaSet_Class.R.

We have fixed this issue.

checkModel.R

[x] Again optional but perhaps this is better placed with the XevaSet_Class.R code.

The position of the code has been changed.

creat_Experiment_slot.R

[x] modelClassS4Vars() where did these hard coded values come from?

They are from Meehan, et al. Cancer research 77.21 (2017). Have added a note in the function also

create_drug_slot.R

[x] could this function be combined with a different file to reduce the number of different files? What is the point of this function?

The position of the code has been changed.

create_modToBiobaseMap_slot.R/create_sensitivity_slot.R

[x] Again completely optional but if these are validity methods (which it seems like) then it is probably best to include in the file that has the class definiation.

The position of the code has been changed.

bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

7cf6192 update 7b29fff version bump

bioc-issue-bot commented 5 years ago

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

7cf6192 update 7b29fff version bump

bioc-issue-bot commented 5 years ago

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

45ea3f3 added export of getMolecularProfiles 6390c85 version bump

bioc-issue-bot commented 5 years ago

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

45ea3f3 added export of getMolecularProfiles 6390c85 version bump

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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lshep commented 5 years ago

I just manually kicked off a build so you should get an accurate build report shortly

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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

9473ac7 exported getMolecularProfiles

bioc-issue-bot commented 5 years ago

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

9473ac7 exported getMolecularProfiles

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 5 years ago

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

f9ee441 version bump

bioc-issue-bot commented 5 years ago

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

f9ee441 version bump

bioc-issue-bot commented 5 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.

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Please see the build report for more details.

bioc-issue-bot commented 5 years ago

Dear Package contributor,

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spocks commented 5 years ago

Hi @lshep Please push a manual built for the latest version. I have fixed a minor error from the last manual built. Thanks,

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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gangeshberi commented 5 years ago

@lshep, could you please run a manual build? We have pushed all the changes and we want to see the results now. Thanks!

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Bioconductor / Contributions

Xeva : XEnograft Visualization & Analysis #1022