Closed yiluheihei closed 3 years ago
Hi @yiluheihei
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: microbiomeMarker
Title: microbiome biomarker analysis toolkit
Version: 0.99.0
Authors@R:
person(given = "Yang",
family = "Cao",
role = c("aut", "cre"),
email = "caoyang.name@gmail.com")
Description: To date, a number of methods have been developed for microbiome
marker discovery based on metagenomic profiles, e.g. LEfSe. However, all of
these methods have its own advantages and disadvantages, and none of them is
considered standard or universal. Moreover, different programs or softwares
may be development using different programming languages, even in different
operating systems. Here, we have developed an all-in-one R package
microbiomeMarker that integrates commonly used differential analysis
methods as well as three machine learning-based approaches, including
Logistic regression, Random forest, and Support vector machine, to
facilitate the identification of microbiome markers.
License: GPL-3
biocViews: Metagenomics, Microbiome, DifferentialExpression
URL: https://github.com/yiluheihei/microbiomeMarker
BugReports: https://github.com/yiluheihei/microbiomeMarker/issues
Depends: R (>= 4.1.0)
Imports:
dplyr,
phyloseq,
magrittr,
purrr,
MASS,
utils,
ggplot2,
tibble,
rlang,
stats,
coin,
ggtree,
tidytree,
methods,
IRanges,
tidyr,
patchwork,
ggsignif,
metagenomeSeq,
DESeq2,
edgeR,
BiocGenerics,
Biostrings,
yaml,
biomformat,
S4Vectors,
Biobase,
ComplexHeatmap,
ANCOMBC,
caret,
limma,
ALDEx2,
multtest,
plotROC
Encoding: UTF-8
RoxygenNote: 7.1.1
Roxygen: list(markdown = TRUE)
Suggests:
testthat,
covr,
glmnet,
Matrix,
kernlab,
e1071,
ranger,
knitr,
rmarkdown,
BiocStyle
VignetteBuilder: knitr
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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/microbiomeMarker
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear,
Thanks for your attention. I don't understand why the BiocCheck error appears. The error shows that a Bioconductor package edgeR is not available. However, in my opinion, edgeR should be installed properly in the build machine. Can you help me to point out why this error appears and how to fix it?
Thank your very much.
===============================
BiocCheck('microbiomeMarker_0.99.0.tar.gz')
===============================
This is BiocCheck version 1.29.14. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
cmd: /home/biocbuild/bbs-3.14-bioc/R/bin/R
args: --vanilla CMD INSTALL --no-test-load --library=/tmp/Rtmp9pafK5/file1b130c6b702cd8/lib '/home/pkgbuild/packagebuilder/workers/jobs/2268/microbiomeMarker_20210901195440/microbiomeMarker_0.99.0.tar.gz'
stderr:
ERROR: dependency edgeR is not available for package microbiomeMarker
* removing /tmp/Rtmp9pafK5/file1b130c6b702cd8/lib/microbiomeMarker
* ERROR:
/home/pkgbuild/packagebuilder/workers/jobs/2268/microbiomeMarker_20210901195440/microbiomeMarker_0.99.0.tar.gz
must be installable.
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, :
there is no package called microbiomeMarker
Calls: BiocCheck ... suppressPackageStartupMessages -> withCallingHandlers -> do.call -> <Anonymous>
Execution halted
That does seem like an error on our part. I will try to re-run the build manually and post a new report; hopefully it should resolve itself.
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/microbiomeMarker
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Please note the release schedule that is posted here - http://bioconductor.org/developers/release-schedule/.
We'll try to get your package in before that.
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
suppressWarnings() in R/import-qiime2.R (line 162, column 14)
suppressWarnings() in R/import-qiime2.R (line 217, column 11)
suppressWarnings() in R/lefse-utilities.R (line 168, column 14)
suppressWarnings() in R/plot-postHocTest.R (line 35, column 12)
ok
4 spaces instead of 2 spaces for indents http://bioconductor.org/developers/how-to/coding-style/
remove commented out code
Well written package overall.
Received a valid push on git.bioconductor.org; starting a build for commit id: 0d5f5566e5fa26ac8310bd6c8e9b72098386efca
Hi @nturaga
I really appreciate you taking the time to review the package.
[ ] 1. suppresswarnings()
suppressWarnings()
in R/import-qiime2.R (two times). suppressWarnings()
in R/lefse-utilities.R (line 168, column 14): First, the warning is stating that some variables (features) are collinear, and it is useless to users. Seconde, it will raise lots of warnings since lda is bootstraped in lefse analysis (default 30). Third, the source code of the original lefse implementation also use suppressWarnings()
. Thus, IMO, suppressWarnings()
is necessary.plot_postHocTest()
utilizes ggsignif to add significance brackets to the plot. And said in the README of ggsignif, You can ignore the warning about the missing aesthetics
, which means the warnings is useless to users.[ ] 2. NOTE: Usage of dontrun{} / donttest{} found in man page examples. 2% of man pages use one of these cases.
We use donttest{}
in the example of function run_ancom()
, since the ancom algrithm is time-consuming, since ancom requires to test all pair of features (O(n^2), n is the number of features).
[ ] 4 spaces instead of 2 spaces for indents http://bioconductor.org/developers/how-to/coding-style/.
The codes are reformatted using styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
. However, there are still some (257) lines are not, in rd files due to roxygen2, or in the vignette due to markdown syntax.
[x] remove commented out code
Thanks again for your help. Please let me know if there is anything necessary to be modified.
Best, Yang Cao
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/microbiomeMarker
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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