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BiocBook #3118

Closed js2264 closed 9 months ago

js2264 commented 11 months ago

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

Confirm the following by editing each check box to '[x]'

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bioc-issue-bot commented 11 months ago

Hi @js2264

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: BiocBook
Title: Write, containerize, publish and versionize Quarto books with Bioconductor
Description: 
    A BiocBook can be created by authors (e.g. R developers, but also 
    scientists, teachers, communicators, …) who wish to 1) write (compile a 
    body of biological and/or bioinformatics knowledge), 2) containerize
    (provide Docker images to reproduce the examples illustrated in the compendium), 
    3) publish (deploy an online book to disseminate the compendium), and 4) 
    versionize (automatically generate specific online book versions 
    and Docker images for specific Bioconductor releases). 
Version: 0.99.0
Date: 2023-08-03
Authors@R: 
    person(
        "Jacques", "Serizay", , "jacquesserizay@gmail.com", 
        role = c("aut", "cre")
    )
URL: https://github.com/js2264/BiocBook
BugReports: https://github.com/js2264/BiocBook
Depends:
    R (>= 4.3)
Imports: 
    BiocGenerics, 
    available,
    cli, 
    glue,
    gert, 
    gh, 
    gitcreds,
    httr, 
    usethis,
    dplyr, 
    purrr, 
    tibble, 
    methods, 
    rprojroot, 
    stringr, 
    yaml, 
    tools, 
    utils
Suggests:
    BiocManager, 
    BiocVersion, 
    BiocStyle, 
    rcmdcheck, 
    BiocCheck, 
    sessioninfo,
    knitr,
    quarto,
    testthat (>= 3.0.0)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: 
    Infrastructure, 
    ReportWriting, 
    Software
VignetteBuilder: knitr
License: MIT + file LICENSE
Collate: 
    'doc.R'
    'imports.R'
    'BiocBook.R'
    'BiocBook-methods.R'
    'check.R'
    'editing.R'
    'globals.R'
    'pages.R'
    'utils.R'
Config/testthat/edition: 3
bioc-issue-bot commented 10 months ago

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: ERROR before build products produced.

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

js2264 commented 10 months ago

Hi @hpages thanks for reviewing this package.

The error from the SPB is :

/home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocBook
* checking for file BiocBook/DESCRIPTION ... OK
* preparing BiocBook:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building stub.Rmd using rmarkdown
--- finished re-building stub.Rmd

quarto render ../inst/
make: quarto: No such file or directory
make: *** [Makefile:4: render] Error 127
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted

When running locally on bioconductor_docker:devel, everything works (with some warnings), unless I remove quarto, in which case I can replicate the error from SPB:

root@b2baeba14765:/opt# R CMD build --keep-empty-dirs --no-resave-data BiocBook
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* preparing ‘BiocBook’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘BiocBook_0.99.0.tar.gz’

root@b2baeba14765:/opt# command -V quarto
quarto is /usr/local/bin/quarto

root@b2baeba14765:/opt# mv /usr/local/bin/quarto /usr/local/bin/quarto.bak

root@b2baeba14765:/opt# quarto check
bash: quarto: command not found

root@b2baeba14765:/opt# R CMD build --keep-empty-dirs --no-resave-data BiocBook
* checking for file ‘BiocBook/DESCRIPTION’ ... OK
* preparing ‘BiocBook’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

quarto render ../inst/
make: quarto: No such file or directory
make: *** [Makefile:4: render] Error 127
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
  running 'make' failed
Execution halted

Can you confirm me that the SPB sets up quarto prior to building the package? Thanks

hpages commented 10 months ago

Let me take a look

hpages commented 10 months ago

Ok Quarto is now installed on the Linux builders. Please bump the package version to trigger another build by the SPB.

Note that Quarto is not on the Mac builders yet so we're going to ignore this platform for now (we only build books on Linux at the moment anyways, see https://bioconductor.org/checkResults/3.18/books-LATEST/).

Thanks!

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 19526cec2a81b868f50f826249347c8c3e5c0ff9

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.1.tar.gz

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

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e63f3f49a423fa9e3da135536e41aee838103310

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.2.tar.gz

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

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e30b310b060c3b3e3ddbca6dddac854da90a68d1

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.3.tar.gz

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

js2264 commented 10 months ago

@hpages thanks for setting up quarto on Linux builders. The checks are now all green for Linux, the remaining ERRORs are for Mac, as you mentioned.

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 186e1c5188f91b31a9bc0977e419bee48dd57caf

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.4.tar.gz

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

lshep commented 10 months ago

@js2264 we have temporarily removed the ability to trigger build/check on our system until pending pre-review changes regarding the .gitconfig file are resolved

hpages commented 10 months ago

Thanks Lori @lshep

@js2264 It seems that you still have code that tries to alter the .gitconfig file of the local user e.g. the examples in man/BiocBook.Rd contain:

gert::git_config_global_set('user.name', value = 'js2264')
gert::git_config_global_set('user.email', value = 'jacquesserizay@gmail.com')

Please remove ASAP and make sure that R CMD build and R CMD check do not alter any sensible file on the user machine. Thanks!

bioc-issue-bot commented 10 months ago

cannot build unless issue is open and has the 'pre-review' label or '2. review in progress' label, or is closed and has the 'TESTING' label.

js2264 commented 10 months ago

@lshep Thanks for changing the triggering settings, hopefully this will prevent side effects from any ill-conceived code until this issue is resolved. I apologise again for the trouble this issue is causing to the SPB.

@hpages I have bumped to v0.99.5 on both my origin (https://github.com/js2264/BiocBook/commit/d647bcc30880c98d496ba493872046b730df2458) and Bioc upstream. I have now purged the commands you mentioned from the examples and re-built doc, thank you for pointing this out. I carefully went through the rest of the code to make sure it does not change the git config or other directories for the end user. R CMD build/check should not affect any file from the user machine anymore. I hope I did not miss anything, please let me know if you spot remaining issues. I also tried to comment as much as possible what each command does. Once again, I apologise for messing things up with some poorly thought-out code.

Thanks!

bioc-issue-bot commented 10 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

hpages commented 10 months ago

Thanks @js2264. I just allowed SPB builds/checks again by changing the label to "review in progress". Can you please bump the version again so we get a new build/check report? Thanks

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9a19bdd34a3d10a5b95c44bddc757cc940a94a62

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.6.tar.gz

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

hpages commented 10 months ago

~Hmm... still no SPB report after 9 hours. Any thought @lshep?~ <--- please ignore :flushed:

hpages commented 10 months ago

Ignore my previous comment. I see the report now.

hpages commented 10 months ago

Hi @js2264

BiocBook has a dual nature (from a Bioconductor organizational perspective). It's a software package that contains tools that help the user create their own book. But it's also a book-containing package. This means that if we add it to the software builds and repository, the book it contains won't be deployed so the user won't have access to it. And if we add it to the book builds and repository, then we won't run R CMD check on it (this is not needed on a pure book-containing package) and it's going to make it harder for people who need the software tools to find them.

How can we work around that? Do you think the package could be split in 2 packages? E.g. BiocBook for the software part and BiocBookDemo for the book part, or BiocBookTools for the software part and BiocBook for the book part? In any case the software package would need a traditional vignette (i.e. not Quarto) that covers the tools.

Thanks, H.

js2264 commented 10 months ago

Hi @hpages, how the BiocBook book itself would be deployed (versus the package) is something I had not anticipated, thanks for pointing this out. I can submit an independent BiocBookDemo package containing the book content itself (most of the inst folder) and remove this content from the current BiocBook package, replacing it with more focused vignette(s) instead. Would that work for you?

I take this opportunity to ask: do you reckon a biocViews: Book should be added to template DESCRIPTION for BiocBooks? I am not sure it is actually of any use, but it seems it has been a recommendation at some point for books? Is it a feature actually supported by Bioconductor?

Thanks, J

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1f58ee36bb22345eca73469c9303d83b96fd43e7

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.7.tar.gz macOS 12.6.5 Monterey: BiocBook_0.99.7.tar.gz

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

js2264 commented 10 months ago

@hpages, following your suggestion, I split {BiocBook} in two packages. The initial {BiocBook} package (currently in the SPB) contains the functions to create/edit a BiocBook, and the new {BiocBookDemo} package has been created using BiocBook::init('BiocBookDemo'), and book pages have been migrated from the original {BiocBook} to {BiocBookDemo}.

This means that there is no more gh-pages branch available for {BiocBook} but there is one for {BiocBookDemo}, curretnly serving the devel version of the {BiocBookDemo} online book.

Let me know your thoughts regarding this organization. If this works for you, should I add the BiocBookDemo package to this submission issue with an AdditionalPackage: comment?

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: dcc8c248eda282af3d37f5d1a67a49a54bd88adf

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.8.tar.gz macOS 12.6.5 Monterey: BiocBook_0.99.8.tar.gz

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

hpages commented 10 months ago

I think this organization makes a lot of sense. Yes please submit the new BiocBookDemo package as an additional package. Thanks @js2264 !

js2264 commented 10 months ago

AdditionalPackage: https://github.com/js2264/BiocBookDemo/

bioc-issue-bot commented 10 months ago

Hi @js2264, Thanks for submitting your additional package: https://github.com/js2264/BiocBookDemo. We are taking a quick look at it and you will hear back from us soon.

js2264 commented 10 months ago

@hpages I have added BiocBookDemo to this issue

js2264 commented 10 months ago

Thanks @lshep. Should the "1. awaiting moderation" tag be removed, as this is an additional package and @hpages is already reviewer for the main package? Thanks!

lshep commented 10 months ago

now quite yet -- as I haven't added BiocBookDemo to git and I need the tag to process -- @hpages it should still go into out git.bioconductor.org even tho it is a book correct?

bioc-issue-bot commented 10 months ago

Additional Package has been approved for building.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBookDemo_0.99.0.tar.gz

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

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c2942ac49f50fec7928e809eee5c0f25063852e1

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBookDemo_0.99.1.tar.gz

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

js2264 commented 10 months ago

@lshep thank you very much for handling the submission process and adding BiocBookDemo to git. @hpages the demo book build/check are green (for Linux), and the rendered website can be viewed from the bundle: inst/doc/book/index.html

hpages commented 10 months ago

it should still go into out git.bioconductor.org even tho it is a book correct?

Correct. Thanks @lshep

hpages commented 10 months ago

Thanks @js2264 for splitting the package.

Here is some feedback:

  1. Make sure that you actually need all the packages listed in the Imports and Suggests fields of the BiocBook package. For example are you sure you need to suggest BiocVersion, BiocCheck, or RefManageR, to name a few?

  2. Nothing should get installed from GitHub. Bioconductor packages should always be installed with BiocManager::install(). Trying to install them from GitHub is a recipe for package version mismatches.

  3. BiocBookDemo is not a software package so the biocViews field cannot contain the term Software. Also the Infrastructure and ReportWriting terms are offsprings of the Software term so can't be used either. Unfortunately we still don't have a biocViews vocabulary for book packages (we need to work on it) so let's just drop this field for now.

  4. Add BiocType: Book to BiocBookDemo/DESCRIPTION. We still need to discuss internally what to do about the BiocType field. This field will become redundant with the biocViews field once we have a biocViews ontology for books, so things might change in the future. We'll communicate in the near future about this and it will be easy to adjust the BiocBookDemo/DESCRIPTION file.

  5. About the vignete in the BiocBook software package:

    • Would be nice to have a short introduction that explains what the package is about.

    • Something strange happened to the section numbers: Screenshot from 2023-10-03 13-33-07

      Strangely, the numbers are repeated and the first number is prefixed with 0..

    • The vignette should not show command output in images. Code chunks should be used instead.

    • No need to include all installed packages in the "Session info" section. Just use sessioninfo::session_info(include_base=TRUE). The standard sessionInfo() also works and has the benefit to reduce the number of dependencies.

  6. Found in BiocBookDemo/inst/pages/biocbook-vs-rebook.qmd:

    In fact, this very online book is shipped in the {BiocBook} package, which also provides functions to create/edit books.

    This needs to be updated to reflect the 2-package split. Maybe there are other places in BiocBook and BiocBookDemo where similar updates need to be made?

  7. If you use non-ASCII characters in your DESCRIPTION file (like you do in BiocBook/DESCRIPTION) then you need to specify the encoding of the file before the occurence of the first non-ASCII character. In the case of BiocBook/DESCRIPTION, it seems that the non-ASCII character is the ellipsis used in the Description field. Doesn't seem worth using a specific encoding just for that though, when you can use three dots (...).

Thanks, H.

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5aa4de950e23bffd15b1e231ea7f161e976613cb

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3436c6ac353a3d04ba072537daf18edb2a301aca

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BiocBookDemo_0.99.2.tar.gz

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

bioc-issue-bot commented 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: BiocBook_0.99.9.tar.gz Linux (Ubuntu 22.04.2 LTS): BiocBook_0.99.9.tar.gz

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

js2264 commented 10 months ago

Thanks @hpages for your comments. Here are some answers:

Thank you for pointing out these outdated deps (they should have been deleted after spinning off BiocBookDemo as an independent package. I have removed them as well as other unnecessary ones.

I have corrected BiocBookDemo chapter 2 and the READMEs.

Question:

In BiocBook::init(), I fetch a versioned book template from github: https://github.com/js2264/BiocBook.template/archive/refs/tags/v1.0.4.tar.gz. So strictly speaking, this link is not used to install a package, but kickstart a new one (whose version is preset to 0.98.0) using a github-versioned template. This file is versioned using Github releases: https://github.com/js2264/BiocBook.template/releases. Is this ok? Or should BiocBook.template also be included in Bioconductor, one way or another, and synced with BiocBook versions? The easiest approach I can think of, in order not to have to download this archive from GitHub, would be to include this template as extdata in BiocBook package itself. Would you want me to do this, or would using the github-versioned template be ok?

biocViews field removed entirely. Note that this triggers the "ERROR" in BiocCheck...

BiocType: Book added for future updates.

  1. About the vignete in the BiocBook software package:

I fixed this where needed, thanks for noticing.

Fixed as well.