Closed wenjie1991 closed 2 years ago
Hi @wenjie1991
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: CellBarcode
Type: Package
Title: Cellular DNA Barcode Analysis toolkit
Version: 0.99.3
Authors@R: c(
person("Wenjie", "Sun", email = "sunwjie@gmail.com", role = "cre"),
person("Anne-Marie", "Lyne", email = "Anne-Marie.Lyne@curie.fr", role = "aut"),
person("Leila", "Perie", email = "leila.perie@curie.fr", role = "aut")
)
Description:
This package performs Cellular DNA Barcode (genetic lineage tracing) analysis. The package can handle all kinds of DNA barcodes, as long as the barcode within a single sequencing read and has a pattern which can be matched by a regular expression. This package can handle barcode with flexible length, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing of some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing and meta genome data.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.0.0)
Imports: methods, Rcpp (>= 1.0.5), data.table (>= 1.14.0), plyr (>=
1.8.6), ggplot2 (>= 3.3.5), stringr (>= 1.4.0), magrittr (>=
2.0.1), ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg (>=
0.4.5), Ckmeans.1d.dp (>= 4.3.3), utils, S4Vectors
LinkingTo: Rcpp
RoxygenNote: 7.1.1
Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
biocViews: Preprocessing, QualityControl, Sequencing, CRISPR
Config/testthat/edition: 3
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-08-26 12:20:54 UTC; wsun
Author: Wenjie Sun [cre],
Anne-Marie Lyne [aut],
Leila Perie [aut]
Maintainer: Wenjie Sun <sunwjie@gmail.com>
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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, 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.
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Received a valid push on git.bioconductor.org; starting a build for commit id: fbbec15f7e4810a31ebd2f2671678baf19da2466
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/CellBarcode
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: 92a43a81f223cb427ac91d16ece2afae5fd40ebf
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/CellBarcode
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: 1f8620ef9761d9b41ae0eb218d1d7c6233500127
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/CellBarcode
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
ok
ok
good
ok
ok
NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes.
Please write getters and setter (accessor) functions instead of using direct slot access with @
.
metaname <- rownames(object@metadata)
Received a valid push on git.bioconductor.org; starting a build for commit id: 9f9107cce50bbec895e2c7b3c2509cbf5bdc3fe4
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/CellBarcode
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: 310325348d41354830d0d14f58af27195397aa82
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, 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/CellBarcode
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @nturaga,
General
* If you make the changes by Friday , I'm open to accepting your package in this release cycle.
Thanks for your time. I have made the following changes.
* NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes.
The NOTE has been resolved. No '@' is used in examples or vignettes. Accessor
bc_messyBc
andbc_cleanBc
were introduced to get the slot.* Please write getters and setter (accessor) functions instead of using direct slot access with `@`. ``` metaname <- rownames(object@metadata) ```
There was an accessor function named
bc_names
, which does the job ofrownames(object@metadata)
. We have updated the code to:metaname <- bc_names(object)
And for other cases, such as:
barcodeObj@messyBc <- lapply(barcodeObj@messyBc, function(d) {
d[barcode_seq %in% barcode]
})
We keep using the '@'. We used a lot data.table
object inside the S4 class. And we transform the data.table
to data.frame
in the return of accessors, because we think the data.frame
is more general and is easier to be handled by common users. However, in the code we prefer to keep the data.table
un-transformed, thus keep using '@'.
Thanks,
Received a valid push on git.bioconductor.org; starting a build for commit id: 6ece8dcf7522b08cac8848cbf08927a2e47c85cb
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/CellBarcode
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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