Closed js2264 closed 9 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
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
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.
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
Let me take a look
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!
Received a valid push on git.bioconductor.org; starting a build for commit id: 19526cec2a81b868f50f826249347c8c3e5c0ff9
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: e63f3f49a423fa9e3da135536e41aee838103310
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: e30b310b060c3b3e3ddbca6dddac854da90a68d1
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.
@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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 186e1c5188f91b31a9bc0977e419bee48dd57caf
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.
@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
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!
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.
@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!
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
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
Received a valid push on git.bioconductor.org; starting a build for commit id: 9a19bdd34a3d10a5b95c44bddc757cc940a94a62
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.
~Hmm... still no SPB report after 9 hours. Any thought @lshep?~ <--- please ignore :flushed:
Ignore my previous comment. I see the report now.
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.
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 BiocBook
s? 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
Received a valid push on git.bioconductor.org; starting a build for commit id: 1f58ee36bb22345eca73469c9303d83b96fd43e7
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.
@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?
Received a valid push on git.bioconductor.org; starting a build for commit id: dcc8c248eda282af3d37f5d1a67a49a54bd88adf
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.
I think this organization makes a lot of sense. Yes please submit the new BiocBookDemo package as an additional package. Thanks @js2264 !
AdditionalPackage: https://github.com/js2264/BiocBookDemo/
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.
@hpages I have added BiocBookDemo
to this issue
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!
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?
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.
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: c2942ac49f50fec7928e809eee5c0f25063852e1
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.
@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
it should still go into out git.bioconductor.org even tho it is a book correct?
Correct. Thanks @lshep
Thanks @js2264 for splitting the package.
Here is some feedback:
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?
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.
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.
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.
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:
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.
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?
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5aa4de950e23bffd15b1e231ea7f161e976613cb
Received a valid push on git.bioconductor.org; starting a build for commit id: 3436c6ac353a3d04ba072537daf18edb2a301aca
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.
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.
Thanks @hpages for your comments. Here are some answers:
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?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.
BiocManager::install()
. Trying to install them from GitHub is a recipe for package version mismatches.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 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.biocViews field removed entirely. Note that this triggers the "ERROR" in BiocCheck...
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.BiocType: Book
added for future updates.
[x] Would be nice to have a short introduction that explains what the package is about.
[x] Something strange happened to the section numbers: strangely, the numbers are repeated and the first number is prefixed with 0.
.
[x] The vignette should not show command output in images. Code chunks should be used instead.
[x] 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.
[x] 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.
I fixed this where needed, thanks for noticing.
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 (...
).Fixed as well.
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]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.