Closed nhejazi closed 6 years ago
Hi @nhejazi
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: methyvim
Title: Differential Methylation Analysis with Targeted Minimum Loss-Based
Estimates of Variable Importance Measures
Version: 0.2.3
Authors@R: c(
person("Nima", "Hejazi", email = "nhejazi@berkeley.edu",
role = c("aut", "cre", "cph")),
person("Rachael", "Phillips", email = "rachaelvphillips@berkeley.edu",
role = "ctb"),
person("Alan", "Hubbard", email = "hubbard@berkeley.edu", role = "ctb"),
person("Mark", "van der Laan", email = "laan@stat.berkeley.edu",
role = "aut")
)
Author: Nima Hejazi [aut, cre, cph], Rachael Phillips [ctb], Alan Hubbard [ctb],
Mark van der Laan [aut]
Maintainer: Nima Hejazi <nhejazi@berkeley.edu>
Description: This package provides facilities for differential methylation
analysis based on variable importance measures (VIMs), a class of statistical
target parameters that arise in causal inference. The estimation and inference
procedures provided are nonparametric, relying on ensemble machine learning to
flexibly assess functional relationship among covariates and the outcome of
interest. These tools can be applied to differential methylation at the level
of CpG sites, with valid inference after multiple hypothesis testing.
Depends:
R (>= 3.4.0)
License: file LICENSE
URL: https://github.com/nhejazi/methyvim
BugReports: https://github.com/nhejazi/methyvim/issues
Encoding: UTF-8
LazyData: true
Imports:
stats,
methods,
ggplot2,
gridExtra,
superheat,
wesanderson,
magrittr,
dplyr,
gtools,
tmle,
future,
doFuture,
BiocParallel,
BiocGenerics,
SummarizedExperiment,
GenomeInfoDb,
bumphunter,
IRanges,
limma,
minfi,
methyvimData
Suggests:
testthat,
knitr,
rmarkdown,
BiocStyle,
SuperLearner,
randomForest,
earth,
gam
Remotes:
github::nhejazi/methyvimData
VignetteBuilder: knitr
RoxygenNote: 6.0.1
biocViews:
DNAMethylation,
DifferentialMethylation,
MethylationArray,
MethylSeq
AdditionalPackage: https://github.com/nhejazi/methyvimData
Can't build unless issue is open and '2. review in progress' label is present, or issue is closed and 'TESTING' label is present.
Your package has been approved for building. Your package is now submitted to our queue.
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.
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 following build report for more details:
http://bioconductor.org/spb_reports/methyvim_buildreport_20170829154915.html
Please remove non-R / Bioconductor from your master branch so that, when your package is accepted, only R package files are added to the Bioconductor git repository.
@mtmorgan -- Do you just mean to remove the remotes
section in DESCRIPTION
? Or is there something else that I am missing?
No, the various files CODE_OF_CONDUCT.md etc that are not part of basic R packages structure. Move these to a distinct branch for the duration of the review.
The remotes: field is not supported; your data (package) also needs to be available in CRAN or via Bioconductor. If you're submitting to Bioconductor then the strategy is to submit first the package (usually the experiment data package) that does not depend on the other package, and work through whatever problems cause it not to build. Once building, add the 'AdditionalPackage' field referencing a second package. The workflow is described at https://github.com/Bioconductor/Contributions#submitting-related-packages
Assuming that the data package is the one that can be built independently, I suggest that we close this issue and that you open a new issue with the data package.
Ok -- got it. Sure -- I'll move those files to a separate branch.
The data package that I added above via the "AdditionalPackage" statement is not strictly necessary for this package to build so I don't think we need to close this issue. I'll remove the data package and the remotes field and we should be able to proceed from there.
Received a valid push; starting a build. Commits are:
cf1a1cf version bump after Bioc webhook added
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 following build report for more details:
http://bioconductor.org/spb_reports/methyvim_buildreport_20170829162653.html
Closing this. Will open a new issue and submit the independent data package first.
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
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