Closed CGAO123 closed 9 months ago
Hi @CGAO123
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: TSAR
Type: Package
Title: Thermal Shift Analysis in R
Version: 0.99.0
Date: 2023
Authors@R: c(person("Xinlin",
"Gao",
email = "candygao2015@outlook.com",
role = c("aut", "cre"),
comment = c(ORCID = "0009-0002-2518-235X")),
person(c("William", "M."),
"McFadden",
email = "wmm27@pitt.edu",
role = c("aut","fnd"),
comment = c(ORCID = "0000-0001-6911-2172")),
person(c("Stefan", "G."),
"Sarafianos",
email = "stefanos.sarafianos@emory.edu",
role = c("fnd","aut","ths"),
comment = c(ORCID = "0000-0002-5840-154X"))
)
Description: This package automates analysis workflow for Thermal Shift
Analysis (TSAS) data. Processing, analyzing, and visualizing data through
both shiny applications and command lines. Package aims to simplify
data analysis and offer front to end workflow, from raw data to
multiple trial analysis.
License: AGPL-3
Encoding: UTF-8
LazyData: false
Testthat: true
RoxygenNote: 7.2.3
Imports:
dplyr (>= 1.0.7),
ggplot2 (>= 3.3.5),
ggpubr (>= 0.4.0),
magrittr (>= 2.0.3),
mgcv (>= 1.8.38),
readxl (>= 1.4.0),
stringr (>= 1.4.0),
tidyr (>= 1.1.4),
utils (>= 4.3.1),
shiny (>= 1.7.4.1),
plotly (>= 4.10.2),
shinyjs (>= 2.1.0),
jsonlite (>= 1.8.7),
rhandsontable (>= 0.3.8),
openxlsx (>= 4.2.5.2),
shinyWidgets (>= 0.7.6),
minpack.lm (>= 1.2.3)
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Software, ShinyApps, Visualization, qPCR
DataRaw: data/qPCR_data1.rda
DataRaw2: data/qPCR_data2.rda
DataRaw3: data/Well_Information.rda
DataRaw4: data/Well_Information_Template.rda
DataRawr: data/example_tsar_data.rda
Depends:
R (>= 4.3.0)
Config/testthat/edition: 3
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.
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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 Build System.
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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.0.tar.gz macOS 12.6.5 Monterey: TSAR_0.99.0.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/TSAR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: b103feb5b45640e3823a06fe57b0bba363ce594a
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.1.tar.gz macOS 12.6.5 Monterey: TSAR_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/TSAR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I am having issues with pushing to bioconductor branch. The error relates having a .rapphistory file in the directory, which I have deleted in my github repo and pushed to upstream devel branch. I have pushed the changes to git@git.bioconductor.org:packages/TSAR
, but it appears from the new build that the change is not reflected. I attempted re-pushing, and I was noted that everything is already up-to-date.
How can I check to make sure that I have the write version in the bioconductor branch.
did you do git rm
to officially delete it and git commit
it accordingly?
I manually deleted the file on github and pushed the changes. Right now, git rm cannot find the deleted file.
Received a valid push on git.bioconductor.org; starting a build for commit id: 0a7db8fc178bfbfd50c63992b27e5e98383dced3
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.2.tar.gz macOS 12.6.5 Monterey: TSAR_0.99.2.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/TSAR
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: cd333a902e0ec667039e0c9c0d001053607773b0
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.3.tar.gz macOS 12.6.5 Monterey: TSAR_0.99.3.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/TSAR
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: 6b913237ac19abcce71b86c54dbb617e2144e0ae
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: TSAR_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.4.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/TSAR
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: dbd7c553d6477d15b66c26826f751236a14a3115
Received a valid push on git.bioconductor.org; starting a build for commit id: 0352f8240c53157f6e366e9a09c311a1e22dd7a4
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
On one or more platforms, the build results were: "WARNINGS, 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 Bioconductor Build System: macOS 12.6.5 Monterey: TSAR_0.99.5.tar.gz Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.5.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/TSAR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.6.tar.gz macOS 12.6.5 Monterey: TSAR_0.99.6.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/TSAR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The package is a fairly well-developed state. I note some issues with Bioconductor's coding requirements, however.
TSAR contains three separate Shiny application regarding, data pre-processing, data analysis, and data visualization.
for
loops. While rarely necessary, they can often be replaced by fast vectorisation. See Vectorize.y
for TSA_average
does not.remotes
and replace by BiocManager which can install from GitHub until a package is accepted into Bioconductor.eval = FALSE
. Please see Evaluated Code Chunks.Received a valid push on git.bioconductor.org; starting a build for commit id: 42fddccd55472eb4010a37733321e3adcdff953f
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: ERROR before build products produced.
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/TSAR
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: 724531673f7e83eabec84e44d9d5c9c4011acabd
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.8.tar.gz macOS 12.6.5 Monterey: TSAR_0.99.8.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/TSAR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi Dario, thank you for reviewing my package.
TSAR stands for Thermal Shift Analysis(TSA) in R. TSA is a type of qPCR data given it is outputted by QuantStudio. However, TSA analyzes a completely different topic, protein unfolding curve, which NormqPCR and HTqPCR do not focus on. I have now updated all my vignettes to include this explanation in the correct vignette structure.
Regarding the three separate shiny applications, they are implemented separately because the workflow can be accessed in all these three different stages independently. I kept them separate so that it is easier for user to exit and re-enter workflow freely given the experiments for TSA analysis usually take place over a long span of time.
Regarding for-loops, I made some edits to remove unnecessary ones. I also added more inline comments to notate the codes better. All match.arg() checks for parameters with limited set of values are implemented now. Proper notation for installing package through biocmanager is also implemented. Lastly, all eval=false on non-shiny command are now removed.
Regarding the provenance of dataset. They are experimentally obtained by me and I have now updated my man pages to include such information.
Thank you so much for the edit suggestions and let me know if there are any other things I can improve on.
Best
There are still some for
loops remaining which can straightforwardly be vectorised.
dataset <- c()
for (i in seq_len(length(data))) {
if (is.data.frame(data[[i]]) == FALSE) {
dataset[[i]] <- data.frame(read.csv(file = toString(data[i]), header = TRUE))
} else {
dataset[[i]] <- data.frame(data[[i]])
}
}
and
tsar_data <- c()
for (i in seq_len(length(dataset))) {
cur <- dataset[[i]]
cur <- mutate(cur, ExperimentFileName = name[i])
tsar_cur <- cur %>% mutate(well_ID = paste(cur$Well.Position, cur$Protein, cur$Ligand, date[i], sep = "_"))
tsar_data <- rbind(tsar_data, tsar_cur)
}
Please consider my illustrative example.
personNames <- c("Adam", "Ben", "Chris")
dataFrameList <- lapply(personNames, function(name) data.frame(Name = name, Age = rpois(1, 30)))
dataFrameCombined <- do.call(rbind, dataFrameList) # rbind all of them once to be memory-efficient.
dataFrameCombined
Received a valid push on git.bioconductor.org; starting a build for commit id: 74ce45d7b6b7b987129b50690c4eb454b5d9cf1f
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: macOS 12.6.5 Monterey: TSAR_0.99.9.tar.gz Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.9.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/TSAR
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: 03f64e9734fcd772a1df6d36859d355b5d55ae72
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.10.tar.gz macOS 12.6.5 Monterey: TSAR_0.99.10.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/TSAR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thank you so much for the suggestion and the example illustration. I have now changed several for-loops to lapply and ensured all tests were passed appropriately. Please let me know of any other plausible enhancements.
There are still some inefficient for
loops remaining that iteratively reallocate memory.
screened <- data.frame()
for (i in unique(section$Well.Position)) {
... ...
screened <- rbind(screened, by_well)
}
and
kept <- data.frame()
for (i in unique(raw_data$Well.Position)) {
... ...
kept <- rbind(kept, by_well)
}
Received a valid push on git.bioconductor.org; starting a build for commit id: 561a75db58e890c4f5606ab1b9998f8050cc87d7
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): TSAR_0.99.11.tar.gz macOS 12.6.5 Monterey: TSAR_0.99.11.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/TSAR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thank you for pointing it out, I have changed these using vectorise. I also removed couple other inefficient for loops I saw. Please let me know if I have missed other plausible enhancements.
The package has been substantially improved.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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