MouseFM - Githubissues

matmu commented 4 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/matmu/MouseFM

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 4 years ago

Hi @matmu

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: MouseFM
Type: Package
Title: In-silico methods for finemapping of genetic regions in inbred mice
Version: 0.1.0
Authors@R: person("Matthias", "Munz", role = c("aut", "cre"), 
    email = "matthias.munz@gmx.de", comment = c(ORCID = "0000-0002-4728-3357"))
Description: This package provides methods for genetic finemapping 
    in inbred mice by taking advantage of their very high homozygosity rate (>95%). 
Encoding: UTF-8
LazyData: false
BugReports: https://github.com/matmu/MouseFM/issues
Depends: R (>= 4.0.0)
License: GPL-3
VignetteBuilder: knitr
biocViews: 
    Genetics, 
    SNP, 
    GeneTarget, 
    VariantAnnotation, 
    GenomicVariation, 
    MultipleComparison, 
    SystemsBiology, 
    MathematicalBiology, 
    PatternLogic,
    GenePrediction,
    BiomedicalInformatics,
    FunctionalGenomics
Suggests:
    BiocStyle,
    testthat,
    knitr,
    rmarkdown
Imports:
    httr,
    curl,
    GenomicRanges,
    dplyr,
    ggplot2,
    reshape2,
    scales,
    gtools,
    tidyr,
    data.table,
    jsonlite,
    rlist,
    GenomeInfoDb,
    methods,
    biomaRt,
    stats,
    IRanges
RoxygenNote: 7.1.0

bioc-issue-bot commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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

26eb7bd Version 0.99.0

bioc-issue-bot commented 4 years ago

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 commented 4 years ago

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

15916f0 Update

bioc-issue-bot commented 4 years ago

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

ec8203a Update

bioc-issue-bot commented 4 years ago

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.

bioc-issue-bot commented 4 years ago

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 commented 4 years ago

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

c6752d2 Update

bioc-issue-bot commented 4 years ago

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 commented 4 years ago

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

82e2318 V

bioc-issue-bot commented 4 years ago

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.

bioc-issue-bot commented 4 years ago

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

7aec33e Update DESCRIPTION

bioc-issue-bot commented 4 years ago

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.

Kayla-Morrell commented 4 years ago

Hello @matmu,

Thank you for submitting to Bioconductor. Please see the initial review of the package below. Overall, the package looks great! The required changes must be made while the suggested changes do not have to be but we strongly encourage them. Comment back here with updates that have been made and when the package is ready for a re-review.

NAMESPACE

[ ] REQUIRED: There should be imports listed here along with exports. Using importFrom or import in the roxygen documentation will achieve this. The use of importing will limit the need for package::function in your R code.

Vignette

[ ] SUGGESTION: For each of the vignettes, we prefer not to show installation from github, only from Bioconductor (but you can leave it in your README file).
[ ] REQUIRED: For each of the vignettes in the Session Info section, inline code should only use one `. So the first line of that section should be `sessionInfo()` not ```sessionInfo()```.

fetch

[ ] REQUIRED: Line 59, the space before ``` should be removed, it doesn't render properly when the vignette is built.

R code

[ ] SUGGESTION: For formatting purposes, consider shorter lines. There are 114 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting purposes, consider multiples of 4 spaces for line indents. There are 139 lines that are not.

Best, Kayla

bioc-issue-bot commented 4 years ago

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.

bioc-issue-bot commented 4 years ago

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

ea6a65a Update

bioc-issue-bot commented 4 years ago

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.

matmu commented 4 years ago

Dear Kayla,

thanks a lot for reviewing our package. I have fixed the requirements and suggestions. Regarding the formatting of the R code: is there a simple way to autoformat the code according to Bioconductors needs? Otherwise I would like to leave it as it is.

All the best, Matthias

Kayla-Morrell commented 4 years ago

@matmu - At the end of the BiocCheck, we offer these two points for formating:

    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.

Thank you for making the necessary changes. I have re-reviewed the package and everything looks good. Since the formatting points are not required I'm more than happy to accept the package, and you can change in the future if you chose.

Thank you again for your contribution.

bioc-issue-bot commented 4 years ago

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 commented 4 years ago

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/matmu.keys is not empty), then no further steps are required. Otherwise, do the following:

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

https://bioconductor.org/packages/MouseFM

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.

Bioconductor / Contributions

MouseFM #1499

NAMESPACE

Vignette

R code