Closed kpj closed 3 years ago
Hi @kpj
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: dce
Type: Package
Title: Pathway Enrichment Based on Differential Causal Effects
Version: 0.99.0
Authors@R:
c(
person(
given = "Kim Philipp", family = "Jablonski",
role = c("aut", "cre"),
email = "kim.philipp.jablonski@gmail.com",
comment = c(ORCID = "0000-0002-4166-4343")
),
person(
given = "Martin", family = "Pirkl",
role = c("aut"),
email = "0000-0002-4166-4343"
)
)
Maintainer: Kim Philipp Jablonski <kim.philipp.jablonski@gmail.com>
Description: Compute differential causal effects (dce) on (biological) networks.
Given observational samples from a control experiment and non-control (e.g., cancer) for two genes A and B, we can compute differential causal effects with a (generalized) linear regression.
If the causal effect of gene A on gene B in the control samples is different from the causal effect in the non-control samples the dce will differ from zero.
We regularize the dce computation by the inclusion of prior network information from pathway databases such as KEGG.
URL: https://github.com/cbg-ethz/dce
BugReports: https://github.com/cbg-ethz/dce/issues
biocViews:
Software,
StatisticalMethod,
GraphAndNetwork,
Regression,
GeneExpression,
DifferentialExpression,
NetworkEnrichment,
Network,
KEGG
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends:
R (>= 4.0)
Suggests:
knitr,
testthat (>= 2.1.0),
BiocStyle,
formatR,
cowplot,
dagitty,
lmtest,
sandwich,
devtools
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Imports:
stats,
methods,
assertthat,
graph,
pcalg,
purrr,
tidyverse,
Matrix,
ggraph,
tidygraph,
ggplot2,
rlang,
expm,
MASS,
CombinePValue,
edgeR,
epiNEM,
igraph,
metap,
mnem,
naturalsort,
ppcor,
glm2,
graphite,
reshape2,
dplyr,
glue,
Rgraphviz,
harmonicmeanp,
org.Hs.eg.db
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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/dce
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I had a quick look at the package. I see a "publication" noted in the github readme, for which snakemake workflows are provided in inst/scripts. I had a look at a couple of notebooks there and I find there is too little prose description of purpose or outcome for me to understand what is being done. The vignette "Get started" does not provide motivation to engage with the methods.
That's from the vignette. The aesthetics seem to need work, and the interpretation of the result might be explained in text. I'll have another look when the error status clears.
Thanks a lot for your initial feedback!
We have now done the following:
Received a valid push on git.bioconductor.org; starting a build for commit id: 506057c33e81f7a4fae638022c3c081d60a05923
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
git@git.bioconductor.org:packages/dce
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: 2f9e995d3425f555745bc1b2b6b8953de91d7bad
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/dce
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: da20501bb02bd79b395ca82d26b882c637829f5e
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,
when making changes to your repository push to
git@git.bioconductor.org:packages/dce
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@vjcitn: we have addressed your concerns and the builds are passing. Let us know if there are further things to correct :)
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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