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SingleRBookWrapper #1609

Closed LTLA closed 3 years ago

LTLA commented 4 years ago

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

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bioc-issue-bot commented 4 years ago

Hi @LTLA

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: SingleRBookWrapper 
Title: Compilation Wrapper for the SingleR Book
Version: 0.99.1
Date: 2020-08-26
Authors@R: person(role=c("aut", "cre"), "Aaron", "Lun", email = "infinite.monkeys.with.keyboards@gmail.com")
Description: 
    Serves as a vehicle to compile the SingleR book on the Bioconductor
    build machines. Book chapters are transplanted into the vignettes
    subdirectory where the build system can be deceived into compiling them.
    The compiled book is then available in the tarball for deployment on the
    site of your choice.
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
biocViews: ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow
Workflow: True
NeedsCompilation: no
URL: https://github.com/LTLA/SingleRBookWrapper
RoxygenNote: 7.1.0
Imports: AnnotationHub,
  BiocFileCache,
  BiocNeighbors,
  BiocParallel,
  BiocStyle,
  celldex,
  gridExtra,
  igraph,
  knitr,
  ontoProc,
  pheatmap,
  rebook,
  scater,
  scran,
  scRNAseq,
  SingleR,
  TENxPBMCData,
  viridis
LTLA commented 4 years ago

I would also like to know whether we could get some special CNAMEs with the bioconductor.org domain for the GH Pages deployment, e.g., singleR.bioconductor.org. That would make it look nice and official.

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 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: "TIMEOUT, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LTLA commented 4 years ago

I would estimate that this takes about an hour to build on my laptop, hence the timeout.

mtmorgan commented 4 years ago

As we work through this new format, can you add a tag to the DESCRIPTION file

BiocType: Book

@lshep is it feasible to extend the SPB build times for Book (and Workflow) BiocType: to ??? 2 hours? Not sure if the workflows have guidance on this already...

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f91715a41b6b1c520339292914aadadd78fce20d

bioc-issue-bot commented 4 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: "TIMEOUT, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 50a03cd49cf55cdf8648ce45db09e98bf4eee83b

bioc-issue-bot commented 4 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: "TIMEOUT, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 4 years ago

@mtmorgan Yes. The workflows already get an extended time. I'll have to look up what it exactly is. I'll work on implementing

bioc-issue-bot commented 4 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: "TIMEOUT, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1f9efcbdf109f8c0fd7051794e1b975c9762de73

bioc-issue-bot commented 4 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, TIMEOUT, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 30246002051217c35c0c68ab864e0131cf14f97f

bioc-issue-bot commented 4 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, TIMEOUT, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d4b2c2914dd2a4ceafc0ac3297a3ce119ec70786

bioc-issue-bot commented 4 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, 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.

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

LTLA commented 4 years ago

Looks like the errors aren't my fault here.

I wonder whether we could rename this package to just SingleRBook, which would make it easier to find with the new links (similar to how OSCA's link is just http://bioconductor.org/books/devel/OSCA/).

mtmorgan commented 3 years ago

3 October, 2020

Sorry for my very slow response

Of course this is an impressive achievement, congratulations!

Do you think the model for book publication is suffuciently mature that it could be included as a template in biocthis (recently submitted to Bioconductor)?

Likewise, is there a page to be written for http://bioconductor.org/developers/ and as a pull request on https://github.com/Bioconductor/bioconductor.org, maybe in collaboration with @hpages, on book publishing in Bioconductor?

DESCRIPTION

vignettes

vignettes/book

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2166679f00fc9b1e7f0f6e1223a3c9782e327ab0

bioc-issue-bot commented 3 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, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6395adddc310c1e310d22b0d96e69fd929d9587b

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1af8e3085fb963f9d0d00988be47520ea4bd6ede

bioc-issue-bot commented 3 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, TIMEOUT". 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 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, TIMEOUT, 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LTLA commented 3 years ago

Do you think the model for book publication is suffuciently mature that it could be included as a template in biocthis (recently submitted to Bioconductor)?

Likewise, is there a page to be written for http://bioconductor.org/developers/ and as a pull request on https://github.com/Bioconductor/bioconductor.org, maybe in collaboration with @hpages, on book publishing in Bioconductor?

Possibly, though I don't know how much demand there is for this.

The Trojan Action contains all instructions necessary to create a book package from a directory with Rmarkdown files and a DESCRIPTION, so one could imagine generalizing this.

DESCRIPTION

  • The convention is to list packages used only in vignettes, etc., in the Suggests: field

Done.

  • Is software license appropriate for this type of material, or would one rather go for a creative commons (documentation) license? (I don't know the answer to this)

I replaced it with CC BY.

  • Description: I think this should really describe the book, rather than the purpose of the package -- an abstract / introduction paragraph.

Done.

  • During the build process there is a warning

    * checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'SingleRBookWrapper/vignettes/book/SingleR-book.rds'

    avoid this by adding (as appropriate for this version of Bioconductor) Depends: R (>= 4.0)

This should hopefully be fixed by purging the book/ directory of unnecessary files after the build.

vignettes

  • I suggest updating the Makefile so that it copies or moves the build products to inst/doc (or perhaps inst/doc/book) so the machinery for browsing vignettes 'just works' and it is easier to adopt existing infrastructure (e.g., the build system @hpages) to displaying the package and it's product.

Done. In principle, the build system could scrap from inst/docs rather than wherever it's looking now (vignettes/book/docs?). However, inst/docs will also include the compiled stub vignette (see below); so this approach is not entirely clean, though the stub is never referenced from the book HTMLs so it should be fairly harmless.

  • does the product of the Comments.Rmd file end up somewhere in the built 'package'? if so, it should probably be written in a moderately more formal way, including pointing to the location of the book on the Bioconductor web site, assuming that the package is accepted.

Yes. (This is the stub vignette I was referring to.) This file only exists to indicate that R CMD build should try to build the vignette contents. If I remove this file, I cannot get the Makefile to run.

In any case, I stripped it right down. I don't anticipate anyone reading this.

  • Makefile: use quotes "${R_HOME}/bin/R" -e ... to protect against spaces in ${R_HOME}?

Done.

  • Makefile: a small point but since this forms a model for other books, why past tense target compiled rather than, e.g., compile?

I had been thinking that compiled was the dummy target rather than the action.

vignettes/book

  • Surprised to see a second DESCRIPTION / README.md file here

Removed.

  • _bookdown.yml: not sure what the role of repo: is, and whether LTLA/SingleR-book is appropriate?

Removed. This was inherited from the OSCA repo.

  • _output.yml: not really familiar with things, but does it make sesne to enable sharing: via github, twitter, ...?

Done, though I don't know what effect those settings have.

  • It seems like the published work itself, at a page that I presume will be like https://ltla.github.io/SingleRBook/, should start with the information that one would expect at the front of a book -- title, authors, publication date, copywrite (different from license) -- as well as information relevant to this type of resource, e.g., source version, compilation date, R / Bioconductor versions, cannonical (https://git.bioconductor.org/packages/...) as well as other URLs, etc. It would also be helpful to have a formatted citation, doi (once available), etc

Waiting on rebook to build, but once it does, it will look like:

Screenshot from 2020-10-04 12-12-12

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 69da65d889f0fbe9cfba5a05204bc9647ed0a9e8

bioc-issue-bot commented 3 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, TIMEOUT". 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/SingleRBookWrapper to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

mtmorgan commented 3 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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See further instructions at

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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

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

https://bioconductor.org/packages/SingleRBookWrapper

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.

LTLA commented 3 years ago

Are we going to change the name? Ping me and I'll update the DESCRIPTION.

nturaga commented 3 years ago

3 October, 2020

Sorry for my very slow response

  • @lshep / @nturaga can we rename this package to SingleRBook in the issue tracker / git.bioconductor.org ? (NB: the package has been accepted, so it does not need to be renamed in the SPB).

Of course this is an impressive achievement, congratulations!

Do you think the model for book publication is suffuciently mature that it could be included as a template in biocthis (recently submitted to Bioconductor)?

Likewise, is there a page to be written for http://bioconductor.org/developers/ and as a pull request on https://github.com/Bioconductor/bioconductor.org, maybe in collaboration with @hpages, on book publishing in Bioconductor?

DESCRIPTION

  • The convention is to list packages used only in vignettes, etc., in the Suggests: field
  • Is software license appropriate for this type of material, or would one rather go for a creative commons (documentation) license? (I don't know the answer to this)
  • Description: I think this should really describe the book, rather than the purpose of the package -- an abstract / introduction paragraph.

  • During the build process there is a warning

    * checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects:  'SingleRBookWrapper/vignettes/book/SingleR-book.rds'

    avoid this by adding (as appropriate for this version of Bioconductor) Depends: R (>= 4.0)

vignettes

  • I suggest updating the Makefile so that it copies or moves the build products to inst/doc (or perhaps inst/doc/book) so the machinery for browsing vignettes 'just works' and it is easier to adopt existing infrastructure (e.g., the build system @hpages) to displaying the package and it's product.
  • does the product of the Comments.Rmd file end up somewhere in the built 'package'? if so, it should probably be written in a moderately more formal way, including pointing to the location of the book on the Bioconductor web site, assuming that the package is accepted.
  • Makefile: use quotes "${R_HOME}/bin/R" -e ... to protect against spaces in ${R_HOME}?
  • Makefile: a small point but since this forms a model for other books, why past tense target compiled rather than, e.g., compile?

vignettes/book

  • Surprised to see a second DESCRIPTION / README.md file here
  • _bookdown.yml: not sure what the role of repo: is, and whether LTLA/SingleR-book is appropriate?
  • _output.yml: not really familiar with things, but does it make sesne to enable sharing: via github, twitter, ...?
  • It seems like the published work itself, at a page that I presume will be like https://ltla.github.io/SingleRBook/, should start with the information that one would expect at the front of a book -- title, authors, publication date, copywrite (different from license) -- as well as information relevant to this type of resource, e.g., source version, compilation date, R / Bioconductor versions, cannonical (https://git.bioconductor.org/packages/...) as well as other URLs, etc. It would also be helpful to have a formatted citation, doi (once available), etc

Hi @mtmorgan, I'll change the name today.

nturaga commented 3 years ago

@LTLA @mtmorgan , why isn't there a SingleRBook github repo. The only thing I can find is SingleRBook-base.

mtmorgan commented 3 years ago

@nturaga not sure that it matters now that the package is accepted? git.bioconductor.org has packages/SingleRBookWrapper and it needs to be renamed packages/SingleRBook

nturaga commented 3 years ago

Hi @mtmorgan and @LTLA,

This is now done. The package is renamed to SingleRBook and should be available from that name.

The manifest file is also changed.

On Mon, Oct 5, 2020 at 9:10 AM Martin Morgan notifications@github.com wrote:

@nturaga https://github.com/nturaga not sure that it matters now that the package is accepted? git.bioconductor.org has packages/SingleRBookWrapper and it needs to be renamed packages/SingleRBook

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1609#issuecomment-703621075, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAU6QS6NHNAC3BNDBWBVKQTSJHATNANCNFSM4QLMPETQ .