ggtreeExtra

[xiangpin]

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• Repository: https://github.com/YuLab-SMU/ggtreeExtra

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[bioc-issue-bot]

Hi @xiangpin

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: ggtreeExtra
Type: Package 
Title: An R Package To Add Geom Layers On Circular Or Other Layout Tree Of "ggtree"
Version: 0.99.0
Authors@R: c(
      person(given = "Shuangbin", family = "Xu", role = c("aut", "cre"), email = "xshuangbin@163.com", comment = c(ORCID = "0000-0003-3513-5362")),
      person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-6485-8781"))
      )
Description: 'ggtreeExtra' extends the method for mapping and visualizing associated 
    data on phylogenetic tree using 'ggtree'. These associated data can be 
    mapped to circular layout, fan layout, or other layout tree built by 
    'ggtree' with the grammar of 'ggplot2'.
Imports:
    ggplot2,
    utils,
    rlang,
    ggnewscale
Suggests:
    ggtree,
    treeio,
    ggstar,
    patchwork,
    knitr,
    rmarkdown,
    prettydoc,
    markdown
License: GPL-3
Encoding: UTF-8
URL: https://github.com/YuLab-SMU/ggtreeExtra/
BugReports: https://github.com/YuLab-SMU/ggtreeExtra/issues
LazyData: true
ByteCompile: true
Roxygen: list(markdown = TRUE)
biocViews: Software, Visualization, Phylogenetics, Annotation
RoxygenNote: 7.1.1
VignetteBuilder: knitr

[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: "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 git@git.bioconductor.org:packages/ggtreeExtra 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: 01212ec14ea28042a4d6142660e03d251fdccdd7

[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/ggtreeExtra 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: f986d27409b783921782d3fd5d3d17d9462ae4a3

[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/ggtreeExtra 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: ebe599464a4d537deaf42e25c2cca2a98d3a3c33

[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/ggtreeExtra 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: 9eae95c44c4d22f56bd5f1b396e1e440cfa34b69

[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/ggtreeExtra 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: 2e6ebe17a10dde6f39e2b51d80a50af6bd15dad5

[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/ggtreeExtra 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: 743eb5ca85255efd2b0b2e6220e4ce1c4bb60013

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

[mtmorgan]

3 August, 2020

Please revise your package in response to the following notes. When done, please post a comment indicating how you have responded to each.

DESCRIPTION

• good

vignettes

• please mark the code chunk with package installation instructions with eval = FALSE.

• This is a stylistic comment so please ignore if you wish. I find code difficult to read when the indentation is aligned to a (, because the leading space can be large and inconsistent. I would write the code at ggtreeExtra.Rmd:219 as (I think this follows the tidyverse style guide, except with 4-space indentation, https://style.tidyverse.org/pipes.html#long-lines-2)

  p2 <- 
      p1 + 
      geom_fruit_list(
          geom_fruit(
              data = df,
              geom = geom_bar,
              mapping = aes(y=id, x=value, fill=group2),
              orientation = "y",
              stat = "identity"
          ),
          scale_fill_manual(values=c("blue", "red")), # To map group2
          new_scale_fill(), # To initialize fill scale.
          geom_fruit(
              data = dt,
              geom = geom_star,
              mapping = aes(y=id, x=value, fill=group),
              size = 2.5,
              color = NA,
              starstroke = 0
          )
      ) + 
      new_scale_fill()

R

• the style comment above applies to the R code and examples.

• Lines like (method-ggplot-add.R:16

  if (layout=="inward_circular" || flagreverse){orientation <- -1}else{orientation <- 1}

  are excessively compact and difficult to read. I would write as

  if (layout == "inward_circular" || flagreverse) {
      orientation <- -1
  } else {
      orientation <- 1
  }

• At method-ggplot-add.R:25 I would again aim for more consistent spacing, and with breaks at mathematically logical locations (e.g., after an operator rather than mid-way through function arguments).

  dat[[paste0("new_",xid)]] <-
      orientation *
      normxy(refnum=plot$data$x, targetnum=dat[[xid]], ratio=object$pwidth)

• Use of getFromNamespace() seems to be asking for future trouble, since these are not part of the ggplot2 API. Are there no alternatives?

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: a81e8ca1e935e1a4f7290febb1f01ca98f8c3028

[xiangpin]

Thanks for your review. I have revised ggtreeExtra following your suggestions.

vignettes

• The code chunk of installation instructions has been masked using eval=FALSE.
• Yes, the style comment your suggested is easier to read, I have revised it.

R

• I have revised related R function and examples using the style comment your suggested.
• Because the funtions of getFromNamespace are needed by the object of Position of ggplot2, The Position of ggtreeExtra is a extension of Postion of ggplot2, So they also are needed by ggtreeExtra.

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

[mtmorgan]

I see that you have changed the formatting of the specific chunk of code I indicated, but the rest of the code remains unchanged?

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 599c02d2d5377b42c1dfbaf8696fe71bef008fd9

[xiangpin]

I have changed the formatting of the code chunk that I think it is difficult to read.

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

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[xiangpin]

ok, Thank you!

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

https://bioconductor.org/packages/ggtreeExtra

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.

[xiangpin]

Hello, everyone I was pushing a patch version to Bioconductor, but some issues (the following) were generated. To solve the problem, what do I need to do?

Counting objects: 15, done.
Delta compression using up to 12 threads.
Compressing objects: 100% (15/15), done.
Writing objects: 100% (15/15), 1.52 KiB | 519.00 KiB/s, done.
Total 15 (delta 12), reused 0 (delta 0)
remote: Error: Please bump the version again and push.
remote:
remote: The build did not start as expected. If the issue persists,
remote: please reach out at bioc-devel@r-project.org or post on the
remote: Github issue where your package is being reviewed.
remote:
remote: 500 Server Error: Internal Server Error for url: https://issues.bioconductor.org/start_build
remote:
To git.bioconductor.org:packages/ggtreeExtra.git
   7145622..6c32095  master -> master

[lshep]

This has been reported in multiple threads. We are investigating the issue.

[lshep]

Please try again; the issue should be resolved. If you didn't do so already don't forget to pull from git.bioconductor.org to get the version bump changes from the release and resolve any merge conflicts in the DESCRIPTION.

[xiangpin]

Ok, thank you.