scDDboost

[xiuyuma]

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

• Repository: https://github.com/wiscstatman/scDDboost

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[xiuyuma]

@xiuyuma The simple way is use roxygen to create one. See https://cran.r-project.org/web/packages/roxygen2/vignettes/roxygen2.html for Rcpp part.

Thanks @jianhong , have pushed the latest version.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ee16fb2dd56ed2ff96715e4c6466cae184b965d7

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

[jianhong]

Package 'scDDboost' Review

The package passed check and build. It is almost there.

The DESCRIPTION file

• [ ] Important: R version should be no less than 4.2

The NAMESPACE file

• [ ] NOTE: Selective imports using importFrom instead of import all with import.

  • in line 2 import(RcppEigen)
  • in line 3 import(BiocParallel)
  • in line 4 import(SingleCellExperiment)
  • in line 5 import(ellipsis)
  • in line 6 import(vctrs)

• [ ] Important: Package in Depends field not imported from: ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

R code

• [ ] Important: 1:n is not suggested in source code. Use seq_along or seq.int instead.

  • In file R/pdd.R:
    • at line 156 found ' tmp_z1<-table(ccl[1:n1])'

• [ ] NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) suppressWarnings() in R/rwMle.R (line 18, column 13)

Documentation

• [ ] Important: Please double check your vignettes format. Only sessionInfo will be shown in table of contents.

• [ ] NOTE: use '<-' instead of '=' for assignment in sample codes in Rd files.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: be8c854e5e22104b60d9eb8b589b9d13a0cd91ef

[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/scDDboost 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: 1734aa2104d5ba41b2db3b0f4e9ad12057f765f9

[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/scDDboost 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: 4656d86efe7274ce28a36f8ef6f94992f7c08af1

[xiuyuma]

Hi @jianhong,

Thanks for your quick response. I have addressed those issues

The DESCRIPTION file Important: R version should be no less than 4.2

Fixed, now it requires R version >=4.2

The NAMESPACE file NOTE: Selective imports using importFrom instead of import all with import. in line 2 import(RcppEigen) in line 3 import(BiocParallel) in line 4 import(SingleCellExperiment) in line 5 import(ellipsis) in line 6 import(vctrs)

Fixed, the only import used is for RcppEigen since it basically gives a header file for c

Important: Package in Depends field not imported from: ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

Fixed, import functions used from ggplot2

R code Important: 1:n is not suggested in source code. Use seq_along or seq.int instead. In file R/pdd.R: at line 156 found ' tmp_z1<-table(ccl[1:n1])'

Fixed, used seq_len and seq.int instead

NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) suppressWarnings() in R/rwMle.R (line 18, column 13)

Fixed, removed the suppressWarnings function

Documentation Important: Please double check your vignettes format. Only sessionInfo will be shown in table of contents.

Fixed, now table of contents presents other sections

NOTE: use '<-' instead of '=' for assignment in sample codes in Rd files.The DESCRIPTION file

Fixed, examples in Rd are using '<-' instead of '='

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

[jianhong]

Package 'scDDboost' Review

It is almost there.

Documentation

• [ ] Important: Please double check your vignettes format. Only sessionInfo will be shown in table of contents. I think you may want to add a blank space between # and the session title.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 3e6bcae7a0f754d8af86e742c32f976ffa81d32b

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

[xiuyuma]

@jianhong Hi Jianhong,

Thanks, I have added a blank space between the section title and # .

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[jianhong]

@jianhong Hi Jianhong,

Thanks, I have added a blank space between the section title and # .

Congratulations! Thank you for your contribution in Bioconductor!

[xiuyuma]

@jianhong Thanks for your review and advice

[lshep]

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