SigsPack

[fefschumann]

• Repository: https://github.com/bihealth/SigsPack

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[bioc-issue-bot]

Hi @fefschumann

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: SigsPack
Type: Package
Title: Mutational Signature Estimation for Single Samples
Version: 0.99.0
Author: Franziska Schumann <franziska.schumann@student.hpi.de>
Maintainer: Franziska Schumann <franziska.schumann@student.hpi.de>
Description: Single sample estimation of exposure to mutational signatures.
    Exposures to known mutational signatures are estimated for single samples,
    based on quadratic programming algorithms. Bootstrapping the input
    mutational catalogues provides estimations on the stability of these 
    exposures. The effect of the sequence composition of mutational context
    can be taken into account by normalising the catalogues.
License: GPL-3
Encoding: UTF-8
Depends:
  R (>= 3.6)
biocViews:
  SomaticMutation,
  SNP,
  VariantAnnotation,
  BiomedicalInformatics,
  DNASeq
Imports:
  quadprog (>= 1.5-5),
  methods,
  Biobase,
  BSgenome (>= 1.46.0),
  VariantAnnotation (>= 1.24.5),
  Biostrings,
  GenomeInfoDb,
  GenomicRanges,
  rtracklayer,
  SummarizedExperiment,
  graphics,
  stats,
  utils
Suggests:
  IRanges,
  BSgenome.Hsapiens.UCSC.hg19,
  BiocStyle,
  knitr,
  rmarkdown
VignetteBuilder: knitr
BiocViews:
BugReports: https://github.com/bihealth/SigsPack/issues
URL: https://github.com/bihealth/SigsPack
Collate:
  bootstrap_mut_catalogues.R
  cosmicSigs.R
  create_mut_catalogues.R
  decomposeQP.R
  get_context_freq.R
  hg19context_freq.R
  normalize.R
  plot_bootstrapped_exposure.R
  signature_exposure.R
  summarize_exposures.R
  vcf2mut_cat.R
RoxygenNote: 6.1.1
LazyData: true

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[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[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.

[lshep]

Please fix all ERROR/Warnings before @dvantwisk begins a formal review - Your package currently is missing the require NAMESPACE file.

[dvantwisk]

Hello @fefschumann,

Have you made progress with adding a NAMESPACE to your package like explained above? We want to see packages actively being worked on (within a two-week period) or else we need to close the issue. If an issue if closed, it can be re-opened at a later date when the maintainer is ready to make changes.

[fefschumann]

Hi,

we have added a NAMESPACE file and fixed all the errors that are coming up when we build the package on our machine, but it looks like the push wasn't recognized. Do we need to change the version number?

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

edb415e bump version to 0.99.1

[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: "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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

9b5f8b7 git bump up version

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[dvantwisk]

Hi @fefschumann

Here is the review of your package. I think the code is well written and I only have a few concerns with the vignette. Email me back once you have addressed the following issues:

vignettes/SigsPack.Rmd

• [ ] [REQUIRED] You use eval=FALSE multiple times in this vignette. We generally want to see user facing code run by our builders. Is there a reason why you are using this? There are situations where it is acceptable such as when the code opens a ui.
• [ ] [REQUIRED] The line mentioning installing from github for the devel verion can be removed. BiocManager::install(version = "devel") can be used to install devel versions of Bioconductor packages.

[dvantwisk]

Hi, I'm just checking in again since this issue hasn't been updated in a while. Are you making the changes that I prescribed above? We generally like to see packages be actively worked on within a two week period, of we close the issue. Closed issues can be reopened when the package maintainer is ready to continue work on the package. Are you still working on making changes to this package?

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

ee263d1 Addressed reviewers comments, and added files to e... 6d15cbe Addressed reviewers comments, and added files to e...

[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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[fefschumann]

Dear @dvantwisk,

we have addressed the issues you mentioned in your review and pushed the new version.

[dvantwisk]

The changes look good! I'm going to move to accept the package now.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

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

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/fefschumann.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

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("SigsPack"). The package 'landing page' will be created at

https://bioconductor.org/packages/SigsPack

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.