Closed quranwu closed 1 year ago
Hi @quranwu
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: MarZIC
Type: Package
Title: Marginal mediation effects with zero-inflated compositional
mediator
Version: 0.99.1
Authors@R: c(person(given = "Quran",
family = "Wu",
role = c("aut"),
email = "wuquran@ufl.edu"),
person(given = "Zhigang",
family = "Li",
role = c("aut", "cre"),
email = "lzg2151@gmail.com")
)
Description: This package provides a way to estimate and test marginal mediation effects for
zero-inflated compositional mediators. Estimates of Natural Indirect Effect (NIE),
Natural Direct Effect (NDE) of each taxon, as well as their standand errors and
confident intervals, were provided as outputs. Zeros will not be imputed during
analysis.
URL: https://www.mdpi.com/2073-4425/13/6/1049
License: GPL-2
Imports: Rcpp (>= 1.0.9), NlcOptim, S4Vectors, SummarizedExperiment,
betareg, doParallel, foreach, pracma, mathjaxr, dirmult, stats,
parallel
Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
biocViews: Software, Technology, Sequencing, Microbiome
VignetteBuilder: knitr
RdMacros: mathjaxr
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 7.2.2
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-09-09 05:20:46 UTC; quranwu
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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. 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/MarZIC
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: ea591fe502633064d01d487b0b1f8a1ec393b408
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/MarZIC
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 1fb5f821e8241f06da08df1668e53f0658fe4b7a
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, skipped". 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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to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 3a9db6f67c05ceae4f116d24bdb284093dbe6cb9
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/MarZIC
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: a51551d4de45546bac5f7a51eba1e1b34c19430b
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @quranwu
This looks good! The vignette was clear and there are clear examples.
Code:
Whilst the main code to the user is documented but I found it very hard to follow the R and C++ code and workout what it was doing. Could you document this code more carefully so that it readable to someone who doesn't know about the package?
There is quite some uncommented code - can this be remove or is necessary for documentation purposes?
src:
Please check for user interrupts in C++.
vignette:
You should demonstrate the package on a real example (not just simulated data) that is in the format of a SummarisedExperiment
you make the object smaller to make it faster to run but it's hard to utility of the method when simply shown on simulated data.
Hi @quranwu
I wanted to check in if you planned to make any changes. If you do we can keep the issue open otherwise it we may close the issue (can always re-open at a laster date)
Hi,
Sorry I should have informed earlier. I think we can close this issue for now. Thanks!
Quran
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
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