Closed Jfortin1 closed 2 years ago
Hi @Jfortin1
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: crisprBase
Version: 0.99.0
Date: 2021-10-25
Title: Base functions and classes for CRISPR gRNA design
Authors@R: person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre"))
Depends:
utils,
methods,
R (>= 4.1)
Imports:
BiocGenerics,
Biostrings,
GenomicRanges,
IRanges,
stringr
Suggests:
knitr,
rmarkdown,
testthat
biocViews: CRISPR, FunctionalGenomics
Description: Provides S4 classes for general nucleases and CRISPR nucleases.
Several CRISPR-specific genome arithmetic functions are implemented to
help extract genomic coordinates of spacer and protospacer sequences.
Commonly-used CRISPR nuclease objects are provided that can be readily
used in other packages.
License: MIT + file LICENSE
LazyData: TRUE
Encoding: UTF-8
RoxygenNote: 7.1.2
VignetteBuilder: knitr
Collate:
'AllGenerics.R'
'Nuclease-class.R'
'CrisprNuclease-class.R'
'arithmetics.R'
'data.R'
'utils.R'
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Received a valid push on git.bioconductor.org; starting a build for commit id: 801d87327de887acc99d3926c5ea1ef35a5fdc4e
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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@LiNk-NY Hi Marcel, thanks for reviewing this package. The only error now for the package comes from the fact that testthat
does not build on CRAN at the moment.
Hi Jean-Philippe, @Jfortin1
It looks like testthat
should be available on Mac now.
Please bump the version for another build.
I will review your package today.
Best, Marcel
Hi Jean-Philippe, @Jfortin1 Thank you for your submission. Please see the review below. Best regards, Marcel
BiocCheck::BiocCheck()
.LazyData
field from the DESCRIPTION
or set to FALSE
.BugReports
and URL
fields.info
and name
.
Presumably, info
could be renamed to metadata
.Installation
section.if (require(GenomicRanges))
code. GenomicRanges
should be
available for the examples. Otherwise, use library(GenomicRanges)
if not
available.@
in setValidity
errors. These are not meant to be
used by end-users.> covr::package_coverage()
crisprBase Coverage: 70.09%
R/CrisprNuclease-class.R: 46.58%
R/utils.R: 52.86%
R/AllGenerics.R: 61.90%
R/Nuclease-class.R: 74.07%
R/arithmetics.R: 92.38%
Received a valid push on git.bioconductor.org; starting a build for commit id: a307ef91214ecafb5fd2d0331a7f4a8b25ea9346
Dear Package contributor,
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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.
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Thanks @LiNk-NY for your review -- I've improved the package to incorporate your comments and suggestions.
The only exception is leaving LazyData=TRUE
as
CrisprNuclease
objects for CRISPR ecosystem packages (crisprBowtie and crisprDesign), we do want to access SpCas9
by simply calling crisprBase::SpCas9
Hi Jean-Philippe, @Jfortin1
This is not a good argument for using LazyData
. I can see the convenience but for readability's sake, it is best to use data("SpCas9", package = "crisprBase")
instead. This makes the user immediately aware of what is being requested and from where.
Please remember to respond to the review line-by-line. Thank you.
Received a valid push on git.bioconductor.org; starting a build for commit id: 3e34bff1366eb8228313f0e2eac5f0fa867a89f7
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push on git.bioconductor.org; starting a build for commit id: c204c7c2e0f543233930bdb2a01c8542ff83d4bf
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
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@LiNk-NY Hi Marcel, I have now modified the package to use LazyData=False
, and please find below my line-by-line review. The package has now an ERROR because of the DESCRIPTION file being malformed, supposedly. I cannot recapitulate this error locally with BiocCheck 1.31.14. Any idea what could be going on?
info
to metadata
, and change name
to nucleaseName
Received a valid push on git.bioconductor.org; starting a build for commit id: 3b9a6b616cc77ec8846e64e6a7981e1463ecb7d7
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. 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/crisprBase
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi Jean-Philippe, @Jfortin1
Thank you for making those changes. They look good.
Please use dedicated getter functions and avoid using the @
operator in the CrisprNuclease
show method.
The metadata
generic is defined in S4Vectors
and
you can use it to create a method for your class.
Best regards, Marcel
Received a valid push on git.bioconductor.org; starting a build for commit id: e92636129a9ea4690d990d76f96ea8406eb5714c
Hi Marcel @LiNk-NY,
We have now changed the show method for both CrisprNuclease
and Nuclease
to only use getter functions. We were already importing metadata
from S4Vectors
, so we used that. Thanks!
Waiting for the build to finish now.
Best, JP
Hi Jean-Phlippe, @Jfortin1
Sorry for the mix up. The appropriate way to get the metadata
functionality is by adding
contains = "Annotated"
to the class definition.
This will grant you a metadata
method via inheritance so you won't need to define the method.
Best, Marcel
Received a valid push on git.bioconductor.org; starting a build for commit id: 9ff67f49884bb87d270fbd71eb3ea7d801163006
Hi Marcel @LiNk-NY, that's a great suggestion, thank you.
I have now changed the Nuclease
object to extend the Annotated
class, and reused the metadata
method via inheritance. Documentation and vignette are updated as well.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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Thanks!
Thank you for all of your time and feedback, much appreciated!
@LiNk-NY Hi Marcel, It seems the package is not yet building in BioC 3.15 -- is there anything else I should do from my side?
@Jfortin1 nothing else to do from your sorry. I needed to process the accepted packages. I will do that now and it should appear available within the next 48 hours as long as it still install/builds/checks cleanly on the daily builder. Sorry for the delay
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