Closed anfederico closed 5 years ago
Hi @anfederico
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: animalcules
Title: Statistical microbiome analysis on metagenomics data
Version: 0.0.1
Author:
Yue Zhao <yuezh@bu.edu>,
Anthony Federico <anfed@bu.edu>,
W. Evan Johnson <wej@bu.edu>
Maintainer: Yue Zhao <yuezh@bu.edu>
Description:
Statistical microbiome analysis on metagenomics data.
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Depends:
R (>= 3.5.0)
Imports:
assertthat,
shiny,
shinyjs,
DESeq2,
tibble,
caret,
plotly,
ggplot2,
rentrez,
reshape2,
covr,
ape,
vegan,
dplyr,
magrittr,
MultiAssayExperiment,
SummarizedExperiment,
S4Vectors,
XML,
forcats,
scales,
lattice,
glmnet,
tsne,
DMwR,
plotROC,
DT,
utils
Suggests:
BiocCheck,
BiocStyle,
devtools,
knitr,
rmarkdown,
testthat,
usethis
biocViews:
MicrobiomeData,
ReproducibleResearch,
SequencingData
VignetteBuilder: knitr
URL: https://github.com/compbiomed/animalcules
BugReports: https://github.com/compbiomed/animalcules/issues
RoxygenNote: 6.1.1
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please provide a decent Description: of your package in the DESCRIPTION file, and in the vignette a proper abstract (if you're going to have one) and text in addition to code chunks to provide a literate exposition on your package use. Post a comment here when you have addressed these basic Bioconductor requirements.
Sorry about that, should be all set now.
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Received a valid push; starting a build. Commits are:
8e9d518 fix vig
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Received a valid push; starting a build. Commits are:
928c8e9 modify da analysis
Dear Package contributor,
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push; starting a build. Commits are:
ec0d96e fix da and update vignette
Dear Package contributor,
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push; starting a build. Commits are:
899aa42 fix da
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.
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@Kayla-Morrell Hey Kayla, we need your help on this error ("appending gaps is not supported") here. So we run this function in the vignette normally in our system, but it keeps failing in the test, I'm wondering if this is related to the unstable R 3.6? Also, from the previous log, it seems to be an S4Vectors function error, I'm wondering which version of S4Vectors is being used in the test? Thanks a lot :)
@jasonzhao0307 We seem to be seeing this error with many of our packages due to a recent modification to S4Vectors (version 0.21.3). We are working on this issue and it's our hope to have it fixed soon.
@Kayla-Morrell Would you please tell us when this could be fixed? Thank you!
Received a valid push; starting a build. Commits are:
e2fe460 add docs
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@Kayla-Morrell Hi Kayla, we've tried to commit again, so the previous error disappeared, but another DEseq2 related error showed up: "logical subscript contains NAs"
Received a valid push; starting a build. Commits are:
a9c3adf add more docs
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Received a valid push; starting a build. Commits are:
49912ad version bump
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@Kayla-Morrell Could you help us with this? We'd like to reopen the submission.
@anfederico Please version bump to be sure a new build is initiated.
@Kayla-Morrell Thanks
Received a valid push; starting a build. Commits are:
0c67622 Version bump
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Received a valid push; starting a build. Commits are:
5581fc0 Proper gitignore and R dependency
Received a valid push; starting a build. Commits are:
3bcc84f Remove Rproj
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Hello @anfederico,
Thank you for submitting to Bioconductor. Please see the initial review of your package below. Comment back here with updates that have been made and when the package is ready for a re-review. Please keep in mind the deadline to accept packages into this release cycle is 4/24, therefore changes should be made in a timely manner so as to give enough time for a re-revew and any additional changes.
R CMD BiocCheck
Incomplete final line in inst/shiny/utils/ui_util.R
Consider shorter lines, 157 lines are > 80 characters
Consider 4 spaces instead of tabs, 1 line contains tabs
Consider multiples of 4 spaces for line indents, 666 lines are not (FormatR for help)
[ ] REQUIRED: 'LazyData' should be set to 'FALSE'. Having it set to 'TRUE' only slows down the loading of packages with data.
[ ] CLARIFICATION: Make sure the following packages should be imported since they aren't listed in NAMESPACE
[ ] REQUIRED: Add 'methods' and 'stats' to 'Imports'.
[ ] REQUIRED: 'BiocCheck' and 'devtools' do not have to be suggested unless they are used in examples/vignettes.
[ ] REQUIRED: 'Software' related biocViews need to be included in this package. Right now you are using 'ExperimentData' tags.
[ ] REQUIRED: Exported functions should use camel case or underscoring, not '.' since this indicates S3 dispatch.
[ ] SUGGESTION: Be sure that you are only using import()
if many function are used from the package. If only a few functions are used than import them using importFrom()
.
[ ] REQUIRED: Data in '/data' needs to be documented.
[ ] CLARIFICATION: What is the purpose of the file in the 'data-raw' directory.
[ ] REQUIRED: Documentation for the 'inst/extdata' should be included in the 'inst/script' directory. This should be a script that clearly present how the data was generated. It should include source urls and any important information regarding filtering or processing. It can be executable code, sudo code, or text description. The user should be able to download and be able to roughly reproduce the file or object that is present.
[ ] REQUIRED: We prefer to have an 'Introduction' section that serves as an abstract. Remove the 'abstract:' tag from the metadata of the vignette and create an 'Introduction' section with it. Also be sure to include ` ` around the package name so it will be formated as code instead of regular text.
[ ] REQUIRED: Include an 'Installation' section that shows the users how to download and load the package from Bioconductor.
[ ] REQUIRED: The knit options does not have to be a section in your vignette that displays to the user. Add include = FALSE
inside the {r}
so that the code is run but will not be shown in the vignette output.
[ ] SUGGESTION: It can be up to you what you include in the knit options but I would suggest not including message = FALSE
for all code. Messages can be helpful to users as they work through the vignette. Instead I would add this option to the specific chunks of R code that you won't want the message to show. I would suggest adding in the knit options things like collapse = TRUE
and comment = "#>"
.
[ ] REQUIRED: You do not need to load in all of the libraries for your package in your vignette. They will be loaded when they install your package. Please remove this chunk (lines 47-69). The only libraries that should be loaded are the ones that aren't imported and used strictly in your vignette. Then I would load them as needed in the code.
[ ] REQUIRED: Line 88-90, this code should not be commented out. Instead, add the tag eval = FALSE
to {r} so that the code is shown but not evaluated when building the vignette.
[ ] CLARIFICATION: After running the run_animalcules()
function I noticed on the opening page of the shiny app there is no information for the 'Annotation table'. Both 'Counts Table' and 'Taxonomy Table' have descriptive information about them but 'Annotation' does not. I'm not sure if this was intended but it might be something to consider adding.
[ ] SUGGESTION: Line 132, I would do head(result$sam_table)
so that instead of all 50 subjects being shown just the first 6 subjects.
[ ] SUGGESTION: I wouldn't comment out line 259.
[ ] SUGGESTION: I wouldn't comment out line 275.
[ ] SUGGESTION: Line 276, I would also do head(result$table)
here so all subjects aren't printed out.
[ ] CLARIFICATION: For line 324, when I run the code myself is it expected to get a different list of biomarkers than the ones you show? This will then change the plots following. If so, this might be something you point out to the user so they don't think they messed something up.
[ ] REQUIRED: Section 11 - Toy Dataset, this section is not needed and is what should be included in the 'inst/script' directory. This demonstrates how you went from 'animalcules.rds' to 'MAE.rds.
MAE
animalcules-package
diversities
diversities_help
filter_summary_top
find_taxon_mat
read_pathoscope_data
animalcules
[ ] CLARIFICATION: Is the title/description correct for this file?
[ ] REQUIRED: Add runnable example since it is an exported function (it will most likely be the same as 'Usage' but it's good practice to have since some users just go right to examples).
upsample_counts
[ ] REQUIRED: Use vapply()
instead of sapply()
.
[ ] REQUIRED: Use various apply functions instead of for
loops.
[ ] REQUIRED: Use seq_len()
or seq_along()
instead of 1:...
.
[ ] SUGGESTION: If using import
or importFrom
then you don't need to use package::function
in the R code, you can just use the function normally. This will help simplify your code a bit.
[ ] REQUIRED: The functions in 'utils.R' don't need to be exported to the user. Since they are documented already you can add the @keywords interal
which will remove them from the package index.
Best, Kayla
Received a valid push; starting a build. Commits are:
0a18396 Imports, namespace, bugs #35
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