Closed guypwhunt closed 3 years ago
Hi @guypwhunt
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: GEOexplorer
Title: An Interactive Shiny App for Exploratory Data Analysis and Differential Gene Expression of Microarray Gene Expression Data Held in the GEO Database.
Date: 2021/07/07
Version: 0.99.1
Authors@R:
c(person(given = "Guy",
family = "Hunt",
role = c("aut", "cre"),
email = "guypwhunt1992@gmail.com",
comment = c(ORCID = "0000-0002-5217-2678")),
person(given = "Fabrizio",
family = "Smeraldi",
role = c("ctb", "ths")),
person(given = "Michael",
family = "Barnes",
role = c("ctb", "ths")),
person(given = "Rafael",
family = "Henkin",
role = c("ctb", "ths"))
)
Description: GEOexplorer enables exploratory data analysis and differential gene expression of gene expression analysis to be performed on data held in the GEO database. The outputs are interactive graphs. GEOexplorer also contains a shiny app that can be used to perform exploratory data analysis and differential gene expression of gene expression analysis. The development of GEOexplorer was made possible because of the excellent code provided by GEO2R
(https: //www.ncbi.nlm.nih.gov/geo/geo2r/).
License: `use_gpl3_license()
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
URL: https://github.com/guypwhunt/GEOexplorer/
BugReports: https://github.com/guypwhunt/GEOexplorer/issues
RoxygenNote: 7.1.1.9001
biocViews:
Software,
GeneExpression,
mRNAMicroarray,
DifferentialExpression,
Microarray
Imports:
DT,
htmltools,
factoextra,
ggplot2,
heatmaply,
maptools,
pheatmap,
plotly,
scales,
shiny,
shinyBS,
shinyHeatmaply,
stringr,
umap,
GEOquery,
limma,
impute
Suggests:
rmarkdown,
knitr
VignetteBuilder: knitr
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Hi Guy, @guypwhunt
Thank you for your submission. Please fix the typo error in the build report. Below is the package review. Feel free to ask any questions.
Best, Marcel
DESCRIPTION
file
for easier review.License
field.shiny
in the Depends
field since you use the
functions in the package extensively.Biobase
dependency to the DESCRIPTION
when using functions like
exprs
and pData
.shiny
package.library
calls from inside functions (see note in DESCRIPTION
).convertAdjustment
should probably be a lookup table rather
than a series of if
else
statements.app.R
.rsconnect
folder. This should only be on your local computer.Received a valid push on git.bioconductor.org; starting a build for commit id: 1e97b88b858a698817b32455c3ff274a9b2b5485
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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Received a valid push on git.bioconductor.org; starting a build for commit id: 5abaa95272b62300aeade36f74ade3421bc1791b
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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: "WARNINGS, TIMEOUT, 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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Hi Guy, @guypwhunt
Thank you for your submission. Please fix the typo error in the build report. Below is the package review. Feel free to ask any questions.
Best, Marcel
GEOexplorer #2191
DESCRIPTION
- (optional) Keep to the 80 character width limit in the
DESCRIPTION
file for easier review.- Update the
License
field.- Include packages such as
shiny
in theDepends
field since you use the functions in the package extensively.- Add
Biobase
dependency to theDESCRIPTION
when using functions likeexprs
andpData
.NAMESPACE
- The function names are quite long but are these user-level functions?
- Perhaps these funcitons need not be exported given that it is a
shiny
package.vignettes
- Restricting the text to the 80 character-width limit is better for reviewing and even maintaining.
- I think the vignette for a shiny-app package should include screenshots that show the user how to interact with the app and the coding should be minimal.
- Can a user input code from the shiny app?
R
- Remove
library
calls from inside functions (see note inDESCRIPTION
).- The functions provided do not need to be exported for the shiny app, AFAICT.
- Perhaps you may want to separate the analysis and visualization functions from the shiny funcitonality into separate packages?
- Functions like
convertAdjustment
should probably be a lookup table rather than a series ofif
else
statements./
- Please remove the errors folder.
- Sourcing the R files should not be necessary in
app.R
.- Remove the
rsconnect
folder. This should only be on your local computer.tests
- Looks good.
Good morning Marcel
It is nice to E-meet you.
Thank you for the feedback. I have made all the necessary updates.
I am just looking at the check and build bin errors and warnings.
All the best, Guy
Hi Guy, @guypwhunt
Please respond to the review line by line. Thank you for your contribution.
Note. There are still some errors in check
stage of the package. Please resolve those.
Best, Marcel
Received a valid push on git.bioconductor.org; starting a build for commit id: ec0825a4b22fc5afaa8c1bd0f1b0fb35d99e4ce7
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This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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Your package has been built on Linux, Mac, and Windows.
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Good afternoon Marcel @LiNk-NY
I hope you had a lovely weekend.
I have fixed all the check errors and timeouts.
There are a couple of warnings remaining.
Do I need to fix the warnings as well before we proceed to the next step?
Thanks for all your help, it is really appreciated.
All the best, Guy
Received a valid push on git.bioconductor.org; starting a build for commit id: 8b2bdbea23807ec723e2bf039dc1285ee48582f4
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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: "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.
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when making changes to your repository push to
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Received a valid push on git.bioconductor.org; starting a build for commit id: 424532294640a5516112c2a846cd6ef85115201d
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Good afternoon Marcel @LiNk-NY
I fixed all the warnings as well. So ignore my last comment.
What is the next step?
Thanks for all your help.
All the best, Guy
Hi Guy, @guypwhunt
Please respond to the review item by item and mention the changes you've made.
https://github.com/Bioconductor/Contributions/issues/2191#issuecomment-887708814
Thank you!
Best, Marcel
Afternoon Marcel @LiNk-NY
Of course, my friend. Below are the details of the errors, warnings and notes fixed for each version plus the updates.
Description file Reduced lines to 80 characters or less Updated license to standard license specification Depends updated with shiny, limma, Biobase, plotly
Namespace file Remove all unnecessary exports
Vignettes file Reduced lines to 80 characters or less Included screenshots that show the user how to interact with the app
Unit tests The unit tests were consolidated to avoid timeout issues and more scenarios were added
R folder Remove library calls from inside functions Updated convertAdjustment to a lookup table
Additional files Removed unnecessary files
Version 99.2 Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: could not find function "nonInteractiveDesnityPlot" Update: Vignettes spelling error updated
Version 99.3 Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. Update: Vignettes file name updated
Version 99.4 ERROR: Package Source tarball exceeds Bioconductor size requirement. Update: Reduced picture sizes in Vignettes folder
WARNING: The following files are over 5MB in size: 'inst/doc/GEOexplorer.html' Update: Reduced size of large files
ERROR: Maintainer must subscribe to the bioc-devel mailing list. Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel Update: I subscribed to the bioc-devel mailing list
ERROR: Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags. Update: I added the watched tags
Version 99.5 WARNING: Undocumented arguments in documentation object 'nonInteractiveBoxAndWhiskerPlot' platform Undocumented arguments in documentation object 'nonInteractiveUmapPlot' knn Undocumented arguments in documentation object 'sourceServer' input output session Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter Writing R documentation files in the Writing R Extensions manual. Update: Update functions examples with all required variables
Version 99.6 WARNING: Malformed Title field: should not end in a period. Update: Removed the period from the title field
NOTE: Rd file 'calculateDifferentialGeneExpression.Rd': \examples lines wider than 100 characters: fit2 <- calculateDifferentialGeneExpression(gsms, limmaPrecisionWeights, forceNormalization, gsetData, knnDataInput) Update: Remove non-exported Rd files
ERROR: Running examples in GEOexplorer-Ex.R failed Update: Remove non-exported Rd files
ERROR: Running the tests in tests/testthat.R failed. Update: Updated unit tests to look at the length of string responses
Version 99.7 N/A: cosmetic updates
Version 99.8 ERROR: Running the tests in tests/testthat.R failed. Update: Consolidated unit tests to prevent timeout. This reduced the number of API calls required, and therefore reduced the test time but all functions were still tested.
Version 99.9 NOTE: Consider adding importFrom("grDevices", "palette") importFrom("graphics", "abline", "boxplot", "hist", "par", "text") importFrom("stats", "complete.cases", "cor", "model.matrix", "na.omit", "prcomp", "princomp", "quantile") Update: Added import statements to functions, namespace and description files
WARNING: Add non-empty \value sections to the following man pages: man/loadApp.Rd Update: Added value section to loadApp function
NOTE: Consider shorter lines; 409 lines (10%) are > 80 characters long Update: Formatted and reduced lines to less than 80 characters were possible
Additional update: further unit testing added
Version 99.10 ERROR: Running the tests in tests/testthat.R failed. Update: Updated unit testing to look at the length of string responses rather than long string texts.
Version 99.11 Error: package or namespace load failed for GEOexplorer in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called impute Update: Namespace rewritten
ERROR: Running the tests in tests/testthat.R failed. Update: Bug fixes and added additional unit tests for more scenarios
Version 99.12 ERROR: Running the tests in tests/testthat.R failed Update: Removed test_microarrayGseWithPoorDataQuality.R unit test as it required the Sys.setenv("VROOM_CONNECTION_SIZE") to be updated and is largely tested during the test_microarrayGseWithMissingValues.R unit test
Version 99.13 NOTE: calculateTopDifferentiallyExpressedGenes: warning in topTable(fit2, adjust = adjustment, sort.by = "B", number = 250): partial argument match of 'adjust' to 'adjust.method' Update: Updated of 'adjust' to 'adjust.method' in necessary functions
Version 99.14 WARNING: Found the following significant warnings: Warning: replacing previous import ggplot2::last_plot by plotly::last_plot when loading GEOexplorer Warning: replacing previous import shiny::dataTableOutput by DT::dataTableOutput when loading GEOexplorer Warning: replacing previous import shiny::renderDataTable by DT::renderDataTable when loading GEOexplorer Update: Updated of functions and namespace to exclude last_plot from ggplot2 and dataTableOutput and renderDataTable from shiny import
WARNING: Non-standard license specification Update: Updated description file with standard license specification
Let me know if you have any questions or need anything else from my side.
All the best, Guy
Hi Guy, @guypwhunt
Thank you for making those changes.
Please make sure to resolve this note. You can use utils::globalVariables
.
* checking R code for possible problems ... NOTE
interactiveMeanVariancePlot: no visible binding for global variable
‘ID’
interactivePrcompPcaIndividualsPlot: no visible binding for global
variable ‘ID’
interactivePrincompPcaIndividualsPlot: no visible binding for global
variable ‘ID’
sourceServer: no visible binding for '<<-' assignment to ‘gsetData’
sourceServer: no visible binding for global variable ‘gsetData’
sourceServer: no visible binding for '<<-' assignment to
‘expressionData’
sourceServer: no visible binding for global variable ‘expressionData’
sourceServer: no visible binding for '<<-' assignment to ‘dataInput’
sourceServer: no visible binding for global variable ‘dataInput’
sourceServer: no visible binding for '<<-' assignment to ‘knnDataInput’
sourceServer: no visible binding for global variable ‘knnDataInput’
sourceServer : <anonymous>: no visible global function definition for
‘write.csv’
Undefined global functions or variables:
ID dataInput expressionData gsetData knnDataInput write.csv
Consider adding
importFrom("utils", "write.csv")
to your NAMESPACE file.
Your package has been accepted. Thank you for your contribution.
Best regards, Marcel
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
Thanks, Marcel @LiNk-NY
In version 0.99.16 and version 0.99.17 I:
Thanks for all your help.
All the best, Guy
Thank you Guy for following up. :+1: Best, Marcel
No problem Marcel
All the best, Guy
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