Closed wenjie1991 closed 4 months 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: scMitoMut
Title: Single-cell Mitochondrial Mutation Analysis Tool
Version: 0.99.0
Authors@R:
person("Wenjie", "SUN", , "sunwjie@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "https://orcid.org/0000-0002-3100-2346"))
Description: This package is for analysing mitochondrial mutations using single cell omics
data such as scRNASeq and scATACSeq. It provides functions for mutation
filtering and visualization.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports:
data.table,
Rcpp,
magrittr,
plyr,
stringr,
utils,
stats,
methods,
ggplot2,
pheatmap,
zlibbioc,
RColorBrewer,
rhdf5,
readr,
parallel,
grDevices
LinkingTo:
Rcpp,
RcppArmadillo
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, magick, VGAM
Config/testthat/edition: 3
VignetteBuilder: knitr
NeedsCompilation: yes
biocViews: Preprocessing, Sequencing
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): scMitoMut_0.99.1.tar.gz macOS 12.6.5 Monterey: scMitoMut_0.99.1.tar.gz
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Hi, sorry for the delay in the review! This will be completed in the next dew days!
Hi Oliver, no need to worry. There's no rush.
On Tue, Sep 5, 2023 at 2:27 PM Oliver M. Crook @.***> wrote:
Hi, sorry for the delay in the review! This will be completed in the next dew days!
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3095#issuecomment-1706526320, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSL7VREZA4P7363MLEVAVLXY4LCPANCNFSM6AAAAAA24QPF5Y . You are receiving this because you were mentioned.Message ID: @.***>
Looks good! Thanks for the submission, just a couple of things, but the package is great otherwise
no visible bindings ...
notesThank you for reviewing the submission. I'm glad to hear that overall, the package looks great. I appreciate your feedback and would be happy to address any concerns or make necessary adjustments.
@wenjie1991 the deadline for new submission acceptance for the Bioc 3.18 release is this week. Please pushed changes addressing the above issues.
Hello @lshep, Thank you for the reminder. I'm currently jammed by other tasks and will resume the submission process next week. If it's not feasible to release with Bioc 3.18, I am also comfortable waiting until 3.20 ;-)
Hi @ococrook,
Thank you for your comments once again. I have made some changes:
Received a valid push on git.bioconductor.org; starting a build for commit id: 0c57b0ac24b071a4726c0124f2bf43bb9a3f47f9
Dear Package contributor,
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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: scMitoMut_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): scMitoMut_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/scMitoMut
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thanks!
Final comment is that the README.md should indicate its a bioconductor package, how to make issues and how to contribute to the package (if you're open to that).
Then we can move to accept tha package.
best wishes, Olly
Received a valid push on git.bioconductor.org; starting a build for commit id: 59fbac3988a8c506be7b420193d1b9a462725d67
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Your package has been built on the Bioconductor Single Package Builder.
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 Single Package Builder: macOS 12.7.1 Monterey: scMitoMut_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): scMitoMut_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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
@ococrook Thank you for your suggestions; they prompted me to consider aspects I hadn't previously thought of.
The following changes have been implemented:
Wenjie
Received a valid push on git.bioconductor.org; starting a build for commit id: cc019a914aa1d43c01444cb24a2a619a4d261776
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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 Single Package Builder: Linux (Ubuntu 22.04.2 LTS): scMitoMut_0.99.4.tar.gz macOS 12.7.1 Monterey: scMitoMut_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/scMitoMut
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Sorry for the delay can you add that the bioconductor install instructions to the .readme ?
Received a valid push on git.bioconductor.org; starting a build for commit id: a3894b7c8f2232ee5a0d4e552c07460675aedc1f
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.2 LTS): scMitoMut_0.99.5.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/scMitoMut
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The bioconductor install instructions have been added to the readme.
Surprisingly, the updated package got error in macOS platform. I guess it is not scMitoMut package issue for the Error in the Bioconductor Single Package Builder report above. Since the error is about the dependencies in macOS platform and scMitoMut package has passed the biocCheck in Github Action. I will bump version and try it again in another day.
The error may stem from the absence of a binary package for R-devel on the macOS platform, as described here: https://contributions.bioconductor.org/troubleshooting-build-report.html#cran-binaries-not-available-for-r-4.0
Anyway, I am not sure.
yes this is true. some mac binaries are not available yet as they have not been made for r-devel yet. We can ignore the mac error for now.
Received a valid push on git.bioconductor.org; starting a build for commit id: 8ef0b148eef40fb108bf923b39a8b8d79f424243
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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 Single Package Builder: Linux (Ubuntu 22.04.2 LTS): scMitoMut_0.99.6.tar.gz macOS 12.7.1 Monterey: scMitoMut_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/scMitoMut
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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