methylCC: estimating the cell composition in whole blood samples using DNA methylation data

stephaniehicks commented 5 years ago

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Repository: https://github.com/stephaniehicks/methylCC

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bioc-issue-bot commented 5 years ago

Hi @stephaniehicks

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: methylCC
Title: Estimate the cell composition of whole blood in DNA methylation samples
Version: 0.99.0
Authors@R: c(
    person(c("Stephanie", "C."), "Hicks", role = c("aut", "cre"), 
        email = "shicks19@jhu.edu", 
        comment = c(ORCID = "0000-0002-7858-0231")),
    person("Rafael", "Irizarry", role = "aut", 
        comment = c(ORCID = "0000-0002-3944-4309")))
Imports: Biobase, GenomicRanges, IRanges, S4Vectors,
    dplyr, magrittr, minfi, bsseq, quadprog, plyranges, 
    stats, utils, bumphunter, genefilter,
    FlowSorted.Blood.450k, methods,
    IlluminaHumanMethylation450kmanifest,
    IlluminaHumanMethylation450kanno.ilmn12.hg19
Depends: R (>= 3.6)
Suggests: 
    knitr,
    testthat (>= 2.1.0),
    BiocGenerics,
    BiocStyle,
    tidyr,
    ggplot2
Description: A tool to estimate the cell composition
    of DNA methylation whole blood sample measured on any
    platform technology (microarray and sequencing).
biocViews: Microarray, Sequencing, DNAMethylation, 
    MethylationArray, MethylSeq, WholeGenome
VignetteBuilder: knitr
RoxygenNote: 6.1.1
Encoding: UTF-8
License: CC BY 4.0
BugReports: https://github.com/stephaniehicks/methylCC/
URL: https://github.com/stephaniehicks/methylCC/

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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This is the automated single package builder at bioconductor.org.

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bioc-issue-bot commented 5 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.

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bioc-issue-bot commented 5 years ago

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

81803ec fixing bugs in bioc build

bioc-issue-bot commented 5 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 5 years ago

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

c30c08f trying again

bioc-issue-bot commented 5 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 5 years ago

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

5c71e6d shortening the run time of examples by saving smal...

bioc-issue-bot commented 5 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.

lshep commented 5 years ago

I don't have many comments.

build report

[ ] Fix the global variable and functions NOTE
[ ] Please fix the NOTE about package in more than one field in DESCRIPTION

NEWS

[ ] We would prefer sections take the form recommeneded in ?news where headers don't include the package name and are changes in version as the package name is redundent information

Cheers

bioc-issue-bot commented 5 years ago

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

5f7b140 adding demo argument for examples in package

bioc-issue-bot commented 5 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.

stephaniehicks commented 5 years ago

Hi @lshep

I have address your comments:

[X] In build report, the global variables and functions NOTE are fixed [X] In build report, the note about more than one field in DESCRIPTION is fixed [X] In NEWS, the section headers have the name of the package removed.

Please let me know if there are any other comments or suggestions for things to change. Thanks for your help!

Stephanie

bioc-issue-bot commented 5 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 5 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/stephaniehicks.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("methylCC"). The package 'landing page' will be created at

https://bioconductor.org/packages/methylCC

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

methylCC: estimating the cell composition in whole blood samples using DNA methylation data #1278