Closed Honchkrow closed 2 years ago
Hi @Honchkrow
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: SignacSlim
Type: Package
Title: The slim version of signac.
Version: 0.99.0
Authors@R: c(
person(given = 'Wei', family = 'Zhang', email = 'w-zhang16@tsinghua.org.cn', role = c('aut', 'cre'))
)
Maintainer: Wei Zhang <w-zhang16@tsinghua.org.cn>
Description: The slim version of signac.
The package contains the basic classes and methods from SeuratObject,
Seurat and Signac. This package aims to provide upstream function
for developing the scATAC-seq algorithm.
Depends: R (>= 4.1.0), methods, Rcpp, RcppEigen
License: GPL-3 | file LICENSE
Encoding: UTF-8
LinkingTo: Rcpp, RcppEigen
Imports: Rcpp, RcppEigen, GenomeInfoDb, GenomicRanges, IRanges, Matrix,
Rsamtools, fastmatch, future, future.apply, pbapply, tidyr,
BiocGenerics, SeuratObject, biovizBase, dplyr, hdf5r, stringi,
stats, tools, S4Vectors, data.table, methods, ggplot2
Suggests: knitr, testthat
RoxygenNote: 7.1.2
SystemRequirements: C++11
Collate: 'FeatureMatrix.R' 'NucleosomeSignal.R' 'RcppExports.R'
'generics.R' 'fragments.R' 'genomeinfodb-methods.R'
'granges-methods.R' 'iranges-methods.R' 'objects.R'
'reexports.R' 'region-enrichment.R' 'utilities.R'
'visualization.R'
biocViews: Software, Sequencing, ATACSeq, WholeGenome, SingleCell
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-03-26 13:07:53 UTC; zhang
Author: Wei Zhang [aut, cre]
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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: "WARNINGS, 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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Authors@R: c(
person(given = 'Wei', family = 'Zhang', email = 'w-zhang16@tsinghua.org.cn', role = c('aut', 'cre'))
)
Maintainer: Wei Zhang <w-zhang16@tsinghua.org.cn>
The Maintainer data will be computed by R CMD build. Omit from DESCRIPTION
Received a valid push on git.bioconductor.org; starting a build for commit id: a9726028681eba7b82cbb71874ce8c59d68141fe
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: "WARNINGS". 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/SignacSlim
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: 32a88875e7fe9d6b55cd93f8bd42e4a1f50d492a
We are having trouble with our windows builder that prevented the build from posting. You can check your results at this location: http://staging.bioconductor.org:8000/jobs/1664/
Received a valid push on git.bioconductor.org; starting a build for commit id: 558901af822cd6f5b11bbf68fb5ba895fb237752
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/SignacSlim
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @Honchkrow,
I've got concerns with this package being hosted by Bioconductor.
Firstly, and most importantly: are you coordinating with the Seurat and signac authors (@andrewwbutler, @mojaveazure, @timoast and others) on SignacSlim?
From what I understand, you've taken parts of the signac, Seurat/SeuratObject packages, but you've not properly acknowledged the original authors' work (e.g., in the DESCRIPTION
).
Furthermore, depending on the license, while you may not require their explicit consent to make such a package (I am not a lawyer), I think it would be polite to discuss and co-ordinate with the original authors any package that relies so heavily on their hard work.
E.g., how do you plan to keep this package in-sync with upstream changes to signac and Seurat/SeuratObject?
You've also opted for a different license to the original package, which while not necessarily forbidden (I'm not a lawyer) does seem odd.
Cheers, Pete
Hi @PeteHaitch ,
Thans for pointting these important issues.
Firt of all, I apologize for using the wrong license. Signac and Seurat used the MIT License which mean I can use, copy, modify and publish under MIT License restriction. I will modify this fatal error immediately. The origin author will be acknowledged in DESCRIPTION and the copy right holder (Tim Stuart) will be listed in LICENSE.md.
Second, I will contact with the original authors to discuss the distribution of this package. If they do not want this package be distributed, I will contact you to close this issue.
Thank for your help again!
Honchkrow
Thanks @PeteHaitch for flagging this!
Hi @Honchkrow
I appreciate your interest in the Signac package and your efforts in making a contribution here, but I would prefer that this package is not hosted on Bioconductor. Making this package broadly available will likely lead to issues for users loading both Signac and SignacSlim due to having classes and functions defined in two places. It's also unclear how SignacSlim will be kept in sync with changes to Signac. I think it may also cause some confusion for users as to where they should ask for support when encountering bugs in the package.
I do agree that the dependency footprint of Signac can be reduced. By far the heaviest dependency is Seurat, and I've now changed Seurat to be a suggested package, along with a couple of other packages that were not used extensively. I would support any efforts to use other package dependencies conditionally and move them to suggested packages if you'd like to contribute a PR to Signac.
Hi @timoast,
Thanks for your rapid reply.
The same class name and incomplete method in SignacSlim do cause troubles when loading Signac. Sorry for not take into account.
I will clsoe this issue. If there any things I should do, for example, delete the package in bioconductor (git@git.bioconductor.org:packages/SignacSlim) or other things, please let me know.
Thanks you again, @PeteHaitch .
Honchkrow
Thank you for considering everyone's feedback, @Honchkrow. I'm sure there are more opportunities to help improve scATAC-seq analysis in Bioconductor and interoperability with signac.
Regarding the package and issue: I don't think there's anything more you need to do.
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