mitoClone2

[benstory]

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[bioc-issue-bot]

Hi @benstory

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: mitoClone2
Type: Package
Title: Clonal population identification in single-cell RNA-seq data
        using mitochondrial and somatic mutations
LinkingTo: Rhtslib (>= 1.13.1)
Version: 0.99.0
Authors@R: c( person(given = "Benjamin", family = "Story", role = c("aut", "cre"), email = "story.benjamin@gmail.com"),
	   person(given = "Lars", family = "Velten", role = "aut"),
	   person(given = "Gregor", family = "Mönke", role = "aut") )
Description: This package primarily identifies variants in mitochondrial genomes from BAM alignment files; filters these variants to remove RNA editing events; estimates their evolutionary relationship (i.e. their phylogenetic tree); groups single cells into clones using a probabilistic approach; visualizes the mutations and provides context in relation to genomic annotations
License: GPLv3
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
biocViews: Annotation, DataImport, Genetics, SNP, Software, SingleCell,
        Alignment
Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices,
        graphics, stats, utils, S4Vectors, Rhtslib, parallel
Suggests: knitr, rmarkdown, Biostrings
RoxygenNote: 7.1.0
SystemRequirements: GNU make, SCITE (optional), PhISCS (optional)
Packaged: 2021-06-20 21:50:22 UTC; story
Depends: R (>= 4.0.0)
NeedsCompilation: yes

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[bioc-issue-bot]

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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ba0696d1903162e48472d8637af31fcc6eab7ca9

[bioc-issue-bot]

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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5b2ad0a48b077f54f954f7883f9eaf10a570ebac

[bioc-issue-bot]

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, 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.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 38f81505ccc4024bbb3101fa88a1f8d464506caa

[bioc-issue-bot]

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, 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.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9129cc48ffca1aa57ea859ab9614621bbf716450

[bioc-issue-bot]

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, 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.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 052ec4c77c3d73ab289c6c3d117b5797ff7b55fa

[bioc-issue-bot]

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, 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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2c3f2c613a57cba6da1881a84ea6663925f80db4

[bioc-issue-bot]

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, 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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d4c67af75d0a303ede1b1d9ede465db794e7a763

[bioc-issue-bot]

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, 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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[benstory]

The package builds on the Mac/Linux machines but not the BioC Windows machine. However, it does build successfully on https://win-builder.r-project.org/.

The only Warning for the Linux/Mac build is related to the included source code from an external program (https://github.com/cbg-ethz/SCITE) and I would prefer not to edit any of their code as a matter of principle. Hervé suggested I include the software since it was so easy to compile - which is a great idea - rather than have the end-user download it on their own. Hopefully this is OK. Please let me know how I can move this process forward.

[hpages]

There was a file permission issue on our Windows builder. It should be addressed now. Please bump the version of the package to trigger a new build by the SPB. Thanks!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 985cf20853f3706eb380b607960501a3f8e0abc8

[bioc-issue-bot]

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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 3e2caae45907de9408b7b0d61fe8285cb68c4b7e

[bioc-issue-bot]

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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2826d1ac9ff4f80b17f405918ff98147a7aad3b0

[bioc-issue-bot]

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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: a23e075484a9319d296c6c2783b47c0f639eae53

[bioc-issue-bot]

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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5de67ffaad0ddc4945aa9e5b8d4be8477fd90d14

[bioc-issue-bot]

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, 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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 6c079ce2aaec0a8a3dcb63b7ff4f402f87d3b360

[bioc-issue-bot]

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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[benstory]

@LiNk-NY

Hi Marcel,

After much trial and tribulation all of those issues have been solved phew. The 'type' and 'gene' error were related to plotting with ggplot2. Hope everything is good.

Thanks again for your time,
Ben

[benstory]

Also feel free to reach out on Slack if anything else needs to be changed - I check it more regularly than github.

[LiNk-NY]

Hi Ben, @benstory

Can anything be done about this warning?

* checking whether package 'mitoClone2' can be installed ... WARNING
Found the following significant warnings:
  ../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
  bam2R_10x.cpp:145:9: warning: ISO C++ forbids variable length array ‘counts’ [-Wvla]
See '/home/user/bioc/mitoClone2.Rcheck/00install.out' for details.

Everything else looks good. Thanks for making those updates!

Best,
Marcel

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 127f59bb8dc1b4769d12a959e590f43b4f663540

[bioc-issue-bot]

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/mitoClone2 to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[benstory]

Hello Marcel @LiNk-NY,

The bam2R_10x warning should be fixed (although I'm not seeing it in the previous build report). The other warning is caused by the SCITE source code - I think it is very much negligible. I would prefer not to modify any of the source code from the external software package - in order to be able to confidently tell the end-user that they are using a clone of the existing SCITE program (https://github.com/cbg-ethz/SCITE) that has not been modified in any way.

Hope that is alright with you. Thanks again for your help in this process.

Best,
Ben

[benstory]

Looking into it a little further - I think it just depends on the compiler. g++ -std=c++11 seems to not give any warnings whereas clang++ does.

[LiNk-NY]

Hi Ben, @benstory

Thank you for making those changes.

Given that you include the SCITE software in your package it is appropriate to include the authors of that software as contributors in the DESCRIPTION file.

I am accepting your package. Thank you for your contribution.
Please make sure to follow up with any feedback from BiocCheck::BiocCheck().

Best regards,
Marcel

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

[benstory]

Awesome thanks for all the help Marcel @LiNk-NY !

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("mitoClone2"). The package 'landing page' will be created at

https://bioconductor.org/packages/mitoClone2

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.