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phemd #897

Closed wschen closed 5 years ago

wschen commented 6 years ago

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bioc-issue-bot commented 6 years ago

Hi @wschen

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: phemd
Type: Package
Title: Phenotypic EMD for comparison of single-cell samples
Version: 0.99.0
Author: William S Chen
Maintainer: William S Chen <wil.yum.chen@gmail.com>
Description: Package for comparing and generating a low-dimensional embedding of multiple single-cell samples 
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends:
Imports: monocle, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, roxygen2, Seurat
Suggests: knitr
VignetteBuilder: knitr
biocViews: Clustering, ComparativeGenomics, Proteomics, Transcriptomics, Sequencing, DimensionReduction, SingleCell, DataRepresentation, Visualization, MultipleComparison
RoxygenNote: 6.1.0

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bioc-issue-bot commented 6 years ago

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mtmorgan commented 6 years ago

Please update your package to interoperate (i.e., accept as inputs) with the SingleCellExperiment and / or SummarizedExperiment objects, and other relevant core Bioconductor classes

bioc-issue-bot commented 6 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 6 years ago

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

152d3ca Version bump

wschen commented 6 years ago

Please update your package to interoperate (i.e., accept as inputs) with the SingleCellExperiment and / or SummarizedExperiment objects, and other relevant core Bioconductor classes

I have extended support for the SingleCellExperiment datatype

bioc-issue-bot commented 6 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 6 years ago

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

43c242d Version bump

bioc-issue-bot commented 6 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 6 years ago

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

cdd3e94 Reorder package loading

bioc-issue-bot commented 6 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 6 years ago

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

020d14b Version bump

bioc-issue-bot commented 6 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.

wschen commented 6 years ago

@LiNk-NY @mtmorgan I have tried to force the use of a prior version of a package (VGAM 1.0-5) as one of the functions was removed in the latest update of the package that is causing the build to fail. The auto-builder does not seem to be allowing this. The VGAM 1.0-5 version is required for one of the Bioconductor packages that my own package is dependent on (Monocle2) and their recommended workaround is what I performed (see below links). I believe this is reason for the build error; I am able to build successfully using my own version of R with VGAM 1.0-5.

https://github.com/cole-trapnell-lab/monocle-release/issues/211 https://github.com/cole-trapnell-lab/monocle-release/issues/188

LiNk-NY commented 6 years ago

Hi William, @wschen We strongly discourage the use of a single version of a package as a dependency (VGAM = 1.0-5). This seems to be an issue for the VGAM maintainer(s).

If your package does not work with future versions of VGAM, I suggest that you find an alternative set of package, if possible.

Regards, Marcel

bioc-issue-bot commented 6 years ago

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

0e05e84 Added missing expression-family function

bioc-issue-bot commented 6 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 6 years ago

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

5637ae8 version bump

bioc-issue-bot commented 6 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 6 years ago

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

4f00ba6 Updated dependencies

bioc-issue-bot commented 6 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.

Please see the build report for more details.

bioc-issue-bot commented 6 years ago

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

ad104b8 Updated documentation 4d69911 Updated documentation 5d3b375 Smaller vignette data

bioc-issue-bot commented 6 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: "WARNINGS, 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 6 years ago

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

0b2289e fixed BioC errors

bioc-issue-bot commented 6 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: "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.

bioc-issue-bot commented 6 years ago

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

aa8d404 Version bump

bioc-issue-bot commented 6 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.

Please see the build report for more details.

bioc-issue-bot commented 6 years ago

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

4b9e044 Imported 'is' command from methods 6b91250 Version bump

bioc-issue-bot commented 6 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: "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.

wschen commented 6 years ago

@LiNk-NY I have addressed all errors and most warnings. The remaining warning is due to a "set.seed" call that I make in a function to ensure reproducibility of results from repeated runs (at a step of random subsampling of data for downstream analyses). I believe that this is preferable to the user but please let me know if you have another solution or recommended change.

Also, is there a specific course of action that I should take to request code review for package acceptance into BioConductor's next release?

LiNk-NY commented 6 years ago

Hi @wschen, I will be reviewing your package. We review them as a first-come-first-serve basis. There are other packages that were submitted before yours.

Thank you.

LiNk-NY commented 6 years ago

Hi William, Thank you for submitting to Bioconductor. I've reviewed your package.

If you have any questions, please respond as a comment to the issue. Thank you, Marcel

phemd #897

DESCRIPTION

NAMESPACE

vignettes/

R/

bioc-issue-bot commented 6 years ago

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

df2dc0e Addressed BioC review concerns

bioc-issue-bot commented 6 years ago

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

e6f9316 Version bump

bioc-issue-bot commented 6 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.

Please see the build report for more details.

bioc-issue-bot commented 6 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: "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.

bioc-issue-bot commented 6 years ago

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

aac3334 Replaced sapply with vapply, updated vignette html...

bioc-issue-bot commented 6 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: "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.

bioc-issue-bot commented 6 years ago

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

89e75c3 Minor fix

wschen commented 6 years ago

@LiNk-NY Thank you for your review and suggestions, Marcel. I have made significant changes and addressed the concerns in a point-wise manner (see below). Hope that my package may still be considered for the upcoming release!

Best, Will

Hi William, Thank you for submitting to Bioconductor. I've reviewed your package.

If you have any questions, please respond as a comment to the issue. Thank you, Marcel

phemd #897

DESCRIPTION

  • Please use the full R.version string 3.5.0 Done.
  • SingleCellExperiment or SummarizedExperiment not in Imports. If you're going to support these data classes, you should be importing the necessary functions to make interoperability possible (assay). Done.
  • Format the file to not exceed 80 column width The "DESCRIPTION" file did not seem to tolerate newline characters to satisfy this suggestion. Is there another way to stay within 80 column width for this file?

NAMESPACE

  • Class names are capitalized by convention. You may also want to remove ('obj') suffix from the name. Changed.
  • The Bioconductor convention is to use camelCase instead of snake_case Changed.

vignettes/

  • Please use a more descriptive title Changed.
  • Consider using BiocStyle::html_document for the vignette build Changed.
  • Remove any mention of biocLite and replace it with BiocManager::install Done.
  • Remove any commented code that is not running. Removed.
  • Stay within the 80 width column limit so that maintaining your vignette and code becomes easier. Done (aside from long url).

R/

  • When working with data_list in get_sample_sizes, it is better to use vapply(data_list, nrow, integer(1L)) rather than an allocate-and-fill for loop Addressed.
  • Remove all instances of semi-colons ; as they are not necessary. Addressed.
  • Consider using a vector of options as the default argument for cell_model and subsequently using match.arg to default to the first or the entered option. Changed.
  • Avoid using a for loop for splitting data, just use split (see ref_clusters) Changed.
  • Use arrow <- for assignment instead of equals sign = Changed.
  • Use lapply and *apply family to work with lists, it saves from for loop object management (for example see indentify_centroids) Changed.
  • Avoid using eval(substitute(...)) for NSE, in gaussianff_local, you can just first calculate the arguments for the new vglmff class ('constraints', 'deviance', etc.) and then use those outputs as inputs to the new function. Changed.
  • Please see the Bioconductor best practices guidelines: http://www.bioconductor.org/developers/package-guidelines/#rcode
  • Avoid using 1:M etc. Done.
  • Replace attach with another verb in attach_seuratobj (e.g., bindSeurat) Done.
  • Please make accessor and setter functions for your object class for example, seuratInfo(phemdObject) and seuratInfo(phemdObject) <- seuratObject. Done.
  • Avoid using @ to access slots Changed except for cases in which it is absolutely necessary (e.g. no accessor function for Seurat@meta.data)
  • Provide validity checks for the phemdObj class to increase robustness. Done.
  • Import the isEmpty generic in S4Vectors to create a method for your phemd class. Done.
  • Plotting functions should not save to the user's file system by default, that can be done by the user's invocation of pdf, png or another desired file format. Done. (Only saves if user specifies save destination which is the non-default setting. Exception is saveSampleHistograms which tends to save tens-hundreds of plots which is not reasonably visualized on a multi-panel plot and requires a user-specified destination directory).
  • Separate methods.R into different files such as plotting.R and other files so that they are easier to manage. Done.
  • Avoid saving intermediate files without the user's consent (dm.RData) Done.
bioc-issue-bot commented 6 years ago

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

17c3b14 Small fix

bioc-issue-bot commented 6 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: "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.

bioc-issue-bot commented 6 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: "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.

bioc-issue-bot commented 6 years ago

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

cba0665 Version bump

bioc-issue-bot commented 6 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: "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.

bioc-issue-bot commented 6 years ago

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

4fd92dd Fixed bug in default parameter selection

bioc-issue-bot commented 6 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: "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.

bioc-issue-bot commented 6 years ago

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

4d40d19 Added vignette pdf and updated readme 1e7d6a0 Merge branch 'master' of https://github.com/wschen...

LiNk-NY commented 6 years ago

Hi William, @wschen Thanks for making those changes. I will accept your package.

Please use the diff below to stay within the 80 character limit.

Also, a few things to work on after the release:

Best regards, Marcel

diff --git a/DESCRIPTION b/DESCRIPTION
index f35c520..6af0e41 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -4,13 +4,45 @@ Title: Phenotypic EMD for comparison of single-cell samples
 Version: 0.99.20
 Author: William S Chen
 Maintainer: William S Chen <wil.yum.chen@gmail.com>
-Description: Package for comparing and generating a low-dimensional embedding of multiple single-cell samples.
+Description: Package for comparing and generating a low-dimensional embedding
+  of multiple single-cell samples.
 License: GPL-2
 Encoding: UTF-8
 LazyData: true
 Depends: R (>= 3.5.0), monocle
-Imports: SingleCellExperiment, RColorBrewer, igraph, transport, pracma, cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree, pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics, stats, utils, cowplot, S4Vectors
+Imports:
+  SingleCellExperiment,
+  RColorBrewer,
+  igraph,
+  transport,
+  pracma,
+  cluster,
+  Rtsne,
+  destiny,
+  Seurat,
+  RANN,
+  ggplot2,
+  maptree, pheatmap,
+  scatterplot3d,
+  VGAM,
+  methods,
+  grDevices,
+  graphics,
+  stats,
+  utils,
+  cowplot,
+  S4Vectors
 Suggests: knitr
 VignetteBuilder: knitr
-biocViews: Clustering, ComparativeGenomics, Proteomics, Transcriptomics, Sequencing, DimensionReduction, SingleCell, DataRepresentation, Visualization, MultipleComparison
+biocViews:
+  Clustering,
+  ComparativeGenomics,
+  Proteomics,
+  Transcriptomics,
+  Sequencing,
+  DimensionReduction,
+  SingleCell,
+  DataRepresentation,
+  Visualization,
+  MultipleComparison
 RoxygenNote: 6.1.0
bioc-issue-bot commented 6 years ago

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

a4b928b Version bump