zzhang23 commented 1 year ago

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

Repository: https://github.com/SalasLab/HiBED

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bioc-issue-bot commented 1 year ago

Hi @zzhang23

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: HiBED
Type: Package
Title: HiBED
Version: 0.99.0
Authors@R: c(person("Ze", "Zhang", role = c("cre", "aut"),
  email = "ze.zhang.gr@dartmouth.edu"),
  person(c("Lucas", "A."), "Salas", role = c("aut"),
  email = "lucas.a.salas.diaz@dartmouth.edu"))
Description: Hierarchical deconvolution for extensive cell type resolution in the human brain 
   using DNA methylation. The HiBED deconvolution estimates proportions up to 7 cell 
   types (GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, 
             oligodendrocytes, endothelial cells, and stromal cells) in bulk brain tissues. 
License: GPL-3
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
biocViews: ExperimentData, Homo_sapiens_Data, Tissue, MicroarrayData, Genome, MethylationArrayData
RoxygenNote: 7.2.1
URL: https://github.com/SalasLab/HiBED
Imports: dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k, minfi
Suggests: knitr, rmarkdown, FlowSorted.CordBlood.450k, testthat

bioc-issue-bot commented 1 year ago

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bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 1 year ago

Hi Ze, @zzhang23 Thank you for your submission. See the review below. Best, Marcel

HiBED #2965

The package needs to make use of existing Bioconductor data representations such as SummarizedExperiment. Currently it only uses matrix. The implementation code needs revision and unit test coverage should be increased.

DESCRIPTION

Add a BugReports field.
Consider adding your ORCiD ID.

NAMESPACE

Looks good.
Consider renaming the main function to the name of the package (i.e., HiBED())

vignettes

Consider including only one data("HiBED_Libraries") call in the vignette. That is, evaluate the data call in line 33 and remove from 46.
Remove the redundant use of print.
Organize your vignette to include Installation and Loading packages sections.

R

Remove the .onLoad function.
Add a @usage section to the HiBED_Libraries documentation as @usage data("HiBED_Libraries")
Please format the code so that it fits the 80 character width limit and remove uncommented code.
Run BiocCheck and adjust the syntax accordingly.
Consider using native pipes |> rather than %>% to avoid the dependency.
Avoid evaluating large chunks of code within the message function
Include the data type in the argument documentation as there are instances where h is character (see line 138 in HiBED_deconvolution.R)
Avoid using data from the .GlobalEnv and follow our recommendations in https://contributions.bioconductor.org

tests

We strongly recommend that you increase coverage

> covr::package_coverage()
HiBED Coverage: 1.37%
R/zzz.R: 0.00%
R/HiBED_deconvolution.R: 1.39%

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a9df953c56e422952a4889af302ba2e31faa945c

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c3b34be82d584fe9682367595a5f6aa5d7852975

bioc-issue-bot commented 1 year 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: "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.

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bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f0fcbe617909e26cd9ec5bb5da3119139cde5666

bioc-issue-bot commented 1 year 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.

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bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8c89b4c6cbcf77b7c08527e92a0e168a87b5762d

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b984d854f3f4a87b043982e76fd6733b25d333e9

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f874228fca1a55e5f3b1ed518290520512e5cbe

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fb3e2542636e4e0067c5f1178be07434350e2127

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

zzhang23 commented 1 year ago

Hi Marcel, @LiNk-NY

Thank you for your review. I believe I have addressed your comments below

HiBED #2965

The package needs to make use of existing Bioconductor data representations such as SummarizedExperiment. Currently it only uses matrix. The implementation code needs revision and unit test coverage should be increased.

I changed the matrices to the format of SummarizedExperiment.

DESCRIPTION

Add a BugReports field. Added.

Consider adding your ORCiD ID. Added.
NAMESPACE

Looks good.

Consider renaming the main function to the name of the package (i.e., HiBED())

vignettes

Consider including only one data("HiBED_Libraries") call in the vignette. That is, evaluate the data call in line 33 and remove from 46. Removed

Remove the redundant use of print. Removed

Organize your vignette to include Installation and Loading packages sections. Updated
R

Remove the .onLoad function. Removed

Add a @usage section to the HiBED_Libraries documentation as @usage data("HiBED_Libraries") Added.

Please format the code so that it fits the 80 character width limit and remove uncommented code. Updated

Run BiocCheck and adjust the syntax accordingly. Updated

Consider using native pipes |> rather than %>% to avoid the dependency. dplyr is imported so this should be fine.

Avoid evaluating large chunks of code within the message function Updated

Include the data type in the argument documentation as there are instances where h is character (see line 138 in HiBED_deconvolution.R) Updated

Avoid using data from the .GlobalEnv and follow our recommendations in https://contributions.bioconductor.org New environment was created to store data.
tests

We strongly recommend that you increase coverage Updated

Please let me know if more things need to be addressed.

Best, Ze

LiNk-NY commented 1 year ago

Hi Ze, @zzhang23

Thank you for making those changes. It looks better. The documentation does not indicate that SummarizedExperiment is a possible input. Please adjust the function so that it can handle both matrix and SummarizedExperiment inputs (you may have to use assay to extract the matrix from the SummarizedExperiment object).

It looks like line 164 in HiBED_deconvolution.R is still looking for h of character type. Please fix this or it will not run if the expected input is numeric.

Best, Marcel

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fbf04027c5a63c200f13bbb85804bbde41666f8b

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 26b5f79cb070760b1ff291d05f840dc6bfe22b95

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

zzhang23 commented 1 year ago

Hi Marcel, @LiNk-NY

Thank you for your time. I misunderstood some of your previous comments but now corrected them accordingly.

Thank you for making those changes. It looks better. The documentation does not indicate that SummarizedExperiment is a possible input. Please adjust the function so that it can handle both matrix and SummarizedExperiment inputs (you may have to use assay to extract the matrix from the SummarizedExperiment object). I updated the function to allow SummarizedExperiment as a possible input.

It looks like line 164 in HiBED_deconvolution.R is still looking for h of character type. Please fix this or it will not run if the expected input is numeric. I corrected h as a numeric variable.

Please let me know if more things are needed. Thanks.

Best, Ze

LiNk-NY commented 1 year ago

Hi Ze, @zzhang23

Sorry for the delay in getting back to you.

Can you please make use of the assay function as mentioned previously? E.g., HiBED_Libraries$Library_Layer1@assays@data@listData$counts should be something like assay(HiBED_Libraries$Library_Layer1, "counts")
consider moving large data packages such as IlluminaHumanMethylation450kmanifest to the Suggests field if the code in the package does not directly need it. It can also be loaded conditionally whenever the function is run (with requireNamespace).

Best, Marcel

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b102179cad9f0b64ebd0199244ceeadf2e82bb21

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

zzhang23 commented 1 year ago

Hi Marcel, @LiNk-NY

Thank you for your feedback. I have made changes accordingly.

Can you please make use of the assay function as mentioned previously? E.g., HiBED_Libraries$Library_Layer1@assays@data@listData$counts should be something like assay(HiBED_Libraries$Library_Layer1, "counts")

I have updated that in lines 56-62 in HiBED_deconvolution.R.

consider moving large data packages such as IlluminaHumanMethylation450kmanifest to the Suggests field if the code in the package does not directly need it. It can also be loaded conditionally whenever the function is run (with requireNamespace).

I have moved IlluminaHumanMethylation450kmanifest and IlluminaHumanMethylationEPICmanifes to the Suggests field.

Let me know if more changes are needed. Thanks a lot.

Best, Ze

LiNk-NY commented 1 year ago

Hi Ze, @zzhang23 Thank you for making those changes.

It seems that the package does not make use of IlluminaHumanMethylation450kmanifest and IlluminaHumanMethylationEPICmanifest. Do they need to be in the Suggests field? It seems to me that they can be removed.

Best, Marcel

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c4200284645e55cd331ae54b7fe378b943b0919f

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8cb568ab802531c9815d7b81d4fde9e357c88f52

bioc-issue-bot commented 1 year 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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zzhang23 commented 1 year ago

Hi Marcel, @LiNk-NY

Thanks for the suggestion.

IlluminaHumanMethylation450kmanifest is actually essential to load our example data but IlluminaHumanMethylationEPICmanifest is redundant. We kept IlluminaHumanMethylation450kmanifest and removed IlluminaHumanMethylationEPICmanifest.

Let me know if more changes are needed.

Best, Ze

LiNk-NY commented 1 year ago

Hi Ze, @zzhang23

Thank you for the update and for making those changes. Please address the NOTE from R CMD check at your earliest convenience.

* checking R code for possible problems ... NOTE
HiBED_deconvolution: no visible global function definition for ‘data’
HiBED_deconvolution: no visible binding for global variable ‘Sum’
Undefined global functions or variables:
  Sum data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Best regards, Marcel

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d46d333589f4d110cd883133657ed3c88e8f7036

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: baf176ca357dbf703646e30e43d467ee8c242027

bioc-issue-bot commented 1 year 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/HiBED to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

zzhang23 commented 1 year ago

Hi Marcel, @LiNk-NY

Please address the NOTE from R CMD check at your earliest convenience. I believe I have addressed the NOTE.

Thank you!

Best, Ze

LiNk-NY commented 1 year ago

Thank you for making those changes. The package has been accepted. Best regards, Marcel

bioc-issue-bot commented 1 year ago

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Bioconductor / Contributions

HiBED #2965

HiBED #2965

DESCRIPTION

NAMESPACE

vignettes

R

tests

HiBED #2965

DESCRIPTION

NAMESPACE

vignettes

R

tests