BayesSpace

[msto]

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• Repository: https://github.com/edward130603/BayesSpace

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[bioc-issue-bot]

Hi @msto

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: BayesSpace
Version: 0.99.0
Date: 2020-09-04
Title: Clustering and Resolution Enhancement of Spatial Transcriptomes
Authors@R: c(
    person("Edward", "Zhao", role=c("aut"), email="[email protected]"),
    person("Matt", "Stone", role=c("aut", "cre"), email="[email protected]"),
    person("Xing", "Ren", role=c("ctb"), email="[email protected]"),
    person("Raphael", "Gottardo", role=c("ctb"), email="[email protected]"))
Maintainer:
    Matt Stone <[email protected]>
Description: Tools for clustering and enhancing the resolution of spatial gene
    expression experiments. BayesSpace clusters a low-dimensional representation
    of the gene expression matrix, incorporating a spatial prior to encourage
    neighboring spots to cluster together. The method can enhance the resolution
    of the low-dimensional representation into "sub-spots", for which features
    such as gene expression or cell type composition can be imputed.
Depends:
    R (>= 4.0.0),
    SingleCellExperiment
Imports:
    Rcpp (>= 1.0.4.6),
    stats,
    BiocSingular,
    purrr,
    scater,
    scran,
    SummarizedExperiment,
    coda,
    rhdf5,
    S4Vectors,
    Matrix,
    assertthat,
    mclust,
    RCurl,
    DirichletReg,
    xgboost,
    utils,
    ggplot2,
    scales
License: MIT + file LICENSE
RoxygenNote: 7.1.0
LinkingTo: 
    Rcpp,
    RcppArmadillo,
    RcppDist,
    RcppProgress
NeedsCompilation: yes
SystemRequirements: C++11
Encoding: UTF-8
Suggests: 
    testthat,
    knitr,
    rmarkdown,
    patchwork,
    igraph
VignetteBuilder: knitr
biocViews:
    Software,
    Clustering,
    Transcriptomics,
    GeneExpression,
    SingleCell,
    ImmunoOncology,
    DataImport
BugReports: https://github.com/edward130603/BayesSpace/issues
URL: edward130603.github.io/BayesSpace

[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".
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
[email protected]:packages/BayesSpace 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: b03c4210d1550fb25656189988d67eae77e8949d

[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
[email protected]:packages/BayesSpace to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[msto]

Hi @mtmorgan,

I've removed the Maintainer: field and subscribed to bioc-devel to address the BiocCheckGitClone and BiocCheck errors.

I'm a bit confused about the remaining issues under macOS.

On the first build, the error was regarding linking to fortran on macOS. I previously encountered a similar issue on my own macbook, and the best solution I was able to find was to install gfortran directly rather than through homebrew. I do have a note in the README suggesting this as a fix, but I'm very open to suggestions for a better solution.

However, on the second build, despite only updating the DESCRIPTION, I no longer receive the same error. Instead, for the check I receive errors that the package is not installable, and the binary build fails because the system cannot find edgeR (an indirect dependency via scran). I'm guessing that the failure to install the package in the CHECK is related to this problem, but I'm not able to replicate it locally. Should I explicitly add edgeR as an import, or do you have another suggestion to fix?

This package does build without issues and pass check/BiocCheck under macOS on the docker image provided in the (semi?)official github action so these should be surmountable problems; unfortunately I'm not familar with the differences between that image and merida1.

Thanks!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ab3372944da45ae3e3fadabd1ee1eb018d97a7d1

[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
[email protected]:packages/BayesSpace to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[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
[email protected]:packages/BayesSpace to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[msto]

Hi @mtmorgan,

The errors appear to have been due to an issue with the Bioconductor build system that Lori Shepherd very helpfully fixed this morning, and the package now builds without error. Please let me know any updates to the package you would suggest when you have time to review.

Thank you!

Matt

[mtmorgan]

Sorry for my slow response

DESCRIPTION

• good

vignettes

• IMPORTANT the code chunks in *.Rmd are not evaluated, enclose the r in braces {r}. Evaluated code chunks are an important part of effective documentation

• do the *bak / *orig and precomile.Rfiles belong in git / at this location?

• From a quick reading, the vignettes would benefit from brief paragraphps interpretting the result of each (or most) code chunks

R (comments on specific lines of code apply throughout)

• Address TODO: in BayesSpace.R

• enhancedFeatures.R:74 use a single warning() statement, perhaps with strwrap() to format output

• readVisium.R:40 stop() calls paste0() internally (use of message(sprintf()) can also often be similarly avoided, so it is usually sufficient to write

  stop("Matrix directory does not exist: ", matrix_dir)
  

  Writing the conditional block on the same line as the conditional leads to long an difficult to read code; follwo the standard convention of writing the body of the conditional on a separate line.

• utils.R:283 caching of internet downloads are relatively easy using BiocFileCache; see the vignette http://bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#local-cache-of-an-internet-resource

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1fb257b7528e44a8bd4338763a54d49764547fb7

[msto]

Hi @mtmorgan,

No worries, thanks for the review!

Description

Thanks!

Vignettes

I had been pre-building some vignettes that were too computationally expensive to expect the user to build during installation. (The *.Rmd.orig files were the raw vignettes, and the precompile.R script knit them into Rmarkdown files where the chunks wouldn't be evaluated.) After getting some helpful feedback in the bioc-community slack, I've removed these vignettes from the package and have made them available on the package's website instead. I think they are helpful, as they reproduce the figures in the accompanying manuscript, but are not necessary to include with the package.

I have updated the remaining vignette so it is evaluated and built upon installation. This vignette demonstrates usage of all exported function in the package.

R

• Address TODO: in BayesSpace.R
  All TODOs have been addressed, removed as deprecated, or deferred for a later release.
• enhancedFeatures.R:74 use a single warning() statement, perhaps with strwrap() to format output
  This has been fixed.
• readVisium.R:40 stop() calls paste0() internally (use of message(sprintf()) can also often be similarly avoided, so it is usually sufficient to write
  All stop(), warning(), and message() statements now avoid use of paste() or paste0().
• Writing the conditional block on the same line as the conditional leads to long an difficult to read code; follwo the standard convention of writing the body of the conditional on a separate line.
  All inline conditionals have been replaced, either by placing the body on a separate line or with ifelse(). (The latter is only used to set default values where appropriate).
• utils.R:283 caching of internet downloads are relatively easy using BiocFileCache; see the vignette
  Thank you very much for this suggestion! This was exactly what I hoped to accomplish and it was very easy to implement.

Please let me know if there are any further updates you'd like us to make to the package prior to acceptance. Thank you!

[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: "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
[email protected]:packages/BayesSpace 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: 46203fa1509ad00c5f75ea9bdf43595e5280905d

[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
[email protected]:packages/BayesSpace to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[msto]

The warning on the previous build was due to R CMD check exceeding the 10 minute runtime limit. I reduced the number of MCMC iterations used in the documentation examples and it now runs in under the limit.

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

[mtmorgan]

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to keep your GitHub and Bioconductor repositories in sync.

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

https://bioconductor.org/checkResults/

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

https://bioconductor.org/packages/BayesSpace

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.

[msto]

Great, thank you Martin!