Open lisiarend opened 1 month ago
Hi @lisiarend
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: PRONE
Type: Package
Title: Normalization and Analysis of Proteomics Data
Version: 0.99.1
Authors@R: c(person("Lis", "Arend", email = "lis.arend@tum.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7990-8385")))
Description: High-throughput omics data are often affected by systematic biases introduced throughout all the steps of a clinical study, from sample collection to quantification.
Normalization methods aim to adjust for these biases to make the actual biological signal more prominent.
However, selecting an appropriate normalization method is challenging due to the wide range of available approaches.
Therefore, a comparative evaluation of unnormalized and normalized data is essential in identifying an appropriate normalization strategy for a specific data set.
This R package provides different functions for preprocessing, normalizing, and evaluating different normalization approaches.
Furthermore, normalization methods can be evaluated on downstream steps, such as differential expression analysis and statistical enrichment analysis.
Spike-in data sets with known ground truth and real-world data sets of biological experiments acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can be analyzed.
License: GPL-3 + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
LazyDataCompression: xz
Depends: R (>= 4.4.0)
Imports:
dplyr,
SummarizedExperiment,
magrittr,
data.table,
RColorBrewer,
ggplot2,
S4Vectors,
ComplexHeatmap,
stringr,
NormalyzerDE,
tibble,
limma,
MASS,
edgeR,
matrixStats,
preprocessCore,
stats,
gtools,
methods,
ROTS,
DEqMS,
ComplexUpset,
tidyr,
purrr,
circlize,
gprofiler2,
plotROC,
MSnbase,
UpSetR,
GGally,
dendsort,
vsn,
Biobase,
reshape2,
POMA,
ggtext,
scales
Suggests:
testthat (>= 3.0.0),
knitr,
rmarkdown,
DT
BugReports: https://github.com/lisiarend/PRONE/issues
URL: https://github.com/lisiarend/PRONE
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Proteomics, Preprocessing, Normalization, DifferentialExpression, Visualization
Is there a way to remove the package down configuration files and docs directory even temporarily for submission so that the Bioconductor branch is a clean branch. It makes it hard to distinguish what a reviewer needs to look into. I am also concerned with a checked in renv.lock file in the top level directory of the package and how it would potentially effect installs/builds of this package as it should not be tied to specific versions but use the latest versions of packages.
It also seems like the LICENSE is just a GPL-3 and not a file LICENSE so this can be updated in the DESCRIPTION
You will also need an inst/script directory that describes how the data in inst/extdata is created. It can be text, pseudo code or code but should describe how a user would re-create data and contain any licensing/source information.
Hey @lshep,
thank you very much for helping me to submit PRONE to Bioconductor.
I removed the package down configuration files, docs directory, and renv.lock file from the main branch.
Furthermore, I removed the file LICENSE from the DESCRIPTION and now only GPL-3 is specified in the DESCRIPTION file. But I still need the LICENSE file in the repository right?
Finally, I added a inst/script directory with a Data.R file showing the code to generate the data in inst/extdata with information on the source of the two data types.
I'm getting the following ERROR now:
PreReview$ R CMD build PRONE
* checking for file 'PRONE/DESCRIPTION' ... OK
* preparing 'PRONE':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file 'renv/activate.R': No such file or directory
Execution halted
-----------------------------------
ERROR: package installation failed
You can or cannot include LICENSE in your package since this license is shipped with R. It can't hurt to include it so leaving it is fine.
Hey @lshep
I apologize for not testing the build after removing the required files. Previously, there was an issue with renv in which was still used in the .Rprofile file, but in the main branch, R CMD build PRONE now works, at least on my end.
We can move this forward however the package currently is unable to be built as dependency DEqMS is unavailable. We have reached out to DEqMS to fix their package but they have thus far been unresponsive. I would encourage you to also reach out to them indicating your need for the package to be fixed for your package review/acceptance to continue as right now that package is a candidate for deprecation as it has not yet built since the Spring release.
Hey @lshep,
I opened an issue on their GitHub (https://github.com/yafeng/DEqMS/issues/16) and removed the DEqMS function from the package. This was only one function, which is not necessarily necessary for the PRONE package but would be a nice feature in the future.
So, the main branch should now be ready to continue the review/acceptance process, and once the DEqMS package is able to be built, I will add the functionality in the next PRONE release again.
Best, Lis
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): PRONE_0.99.1.tar.gz macOS 12.7.1 Monterey: PRONE_0.99.1.tar.gz
Links above 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/PRONE
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hey @lshep,
The build report says that the tarball package size is exceeded. Do you have any recommendations on how to reduce this size without removing the functionalities of my package?
What is the maximum size and how can I see the size of my package in the build report. Do you think it is because of the external data?
Best, Lis Arend
The size is in the summary of the build report. You can also run BiocCheck locally and get more detailed check information in the package.BiocCheck directory that is created (similar to R CMD check). It is likely do to both the data and extdata directories if you look at the information in the report as both those directories are over 4 Mb per R CMD check. We suggest using smaller data sets and or moving data to something like zenodo and then using ExperimentHub to retrieve to use for vignettes/examples/tests
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