signatureSearchData

[yduan004]

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• Repository: https://github.com/yduan004/signatureSearchData

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[bioc-issue-bot]

Hi @yduan004

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: signatureSearchData
Title: Datasets for signatureSearch package
Description: CMAP/LINCS hdf5 databases and other annotations used for 
   signatureSearch software package.
Version: 0.99.1
Author: Yuzhu Duan <yduan004@ucr.edu>
Maintainer: Yuzhu Duan <yduan004@ucr.edu>
Depends: R (>= 3.6)
Imports: AnnotationHub, utils, RSQLite, affy, limma, Biobase, magrittr, dplyr,
         R.utils, stats, methods, rhdf5, SummarizedExperiment
Suggests:knitr, rmarkdown
License: Artistic-2.0
biocViews: AnnotationHub, AnnotationData, FunctionalAnnotation
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 6.1.1

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[yduan004]

The associated software package:

• Repository: https://github.com/yduan004/signatureSearch

[LiNk-NY]

Hi YuZhu, @yduan004 Please see https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages for adding a related package. Thank you, Marcel

[yduan004]

AdditionalPackage: https://github.com/yduan004/signatureSearch

[bioc-issue-bot]

Hi @yduan004,

Starting build on additional package https://github.com/yduan004/signatureSearch.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your additional package repository will NOT trigger a new build.

The DESCRIPTION file of this additional package is:

Package: signatureSearch
Title: Discovering novel modes of action of bioactive compounds
Version: 0.99.5
Date: 2019-03-22
Authors@R: c(person("Yuzhu", "Duan", email = "yduan004@ucr.edu", 
       role = c("aut", "cre")),
       person("Thomas", "Girke", email = "thomas.girke@ucr.edu", 
       role = "aut"))
Description: This package can be used to do Gene Expression Signature Search 
        (GESS) and downstream Functional Enrichment Analysis (FEA).
Depends: R(>= 3.6.0), SummarizedExperiment, Rcpp
Imports: AnnotationDbi, ggplot2, GO.db, GOSemSim (>= 2.0.0), data.table, 
     magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue, stats, 
     utils, org.Hs.eg.db, reshape2, visNetwork, BiocParallel, fastmatch, 
     Biobase, clusterProfiler, readr, gCMAP, DOSE, rhdf5, GSEABase,
     signatureSearchData, AnnotationHub
Suggests: KEGG.db, knitr, testthat, rmarkdown, BiocStyle
License: Artistic-2.0
SystemRequirements: C++11
LinkingTo: Rcpp
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-08-24 18:22:55 UTC; yduan004
biocViews: Software, GeneExpression, GO, KEGG, NetworkEnrichment, 
       Sequencing, Coverage, DifferentialExpression
Maintainer: Yuzhu Duan <yduan004@ucr.edu>
URL: https://github.com/yduan004/signatureSearch/
BugReports: https://github.com/yduan004/signatureSearch/issues

[bioc-issue-bot]

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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[bioc-issue-bot]

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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[lshep]

@LiNk-NY will be handling the formal reviews of your packages. However concerning the software package ERROR.
I think this might stem from the "ah[[" calls scattered throughout the code but not having "ah" globally defined. One approach that might work would be to create a R/zzz.R file with an .onLoad method that defines ah globally

ah <- NULL
.onLoad <- function(...) {
    ah <<- AnnotationHub()
}

Also gCMAP is not supported on windows and therefore your package will also not be supported on windows. If you can avoid utilizing this package as excluding windows will limit your usable audience this is recommended. If you decide to keep the dependency of gCMAP we recommend adding a .BBSoptions file in the top level of your package directory with the line UnsupportedPlatforms: win.

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Received a valid push; starting a build. Commits are:

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[bioc-issue-bot]

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, UNSUPPORTED, 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.

[yduan004]

@LiNk-NY will be handling the formal reviews of your packages. However concerning the software package ERROR. I think this might stem from the "ah[[" calls scattered throughout the code but not having "ah" globally defined. One approach that might work would be to create a R/zzz.R file with an .onLoad method that defines ah globally

ah <- NULL
.onLoad <- function(...) {
    ah <<- AnnotationHub()
}

Also gCMAP is not supported on windows and therefore your package will also not be supported on windows. If you can avoid utilizing this package as excluding windows will limit your usable audience this is recommended. If you decide to keep the dependency of gCMAP we recommend adding a .BBSoptions file in the top level of your package directory with the line UnsupportedPlatforms: win.

Hi Ishep:

Thanks for your help. I have already created the .BBSoptions file to not support windows.

I originally have defined the global ah variable in the utilities.R file:

#' @importFrom AnnotationHub AnnotationHub
ah <- suppressMessages(AnnotationHub())

I could successfully build and check the signatureSearch package on both my local computer and my coworker's. So I think it is not the Error reason. I have not figured out why it fails on the Bioconductor system. But thanks for your help!

Sincerely, Yuzhu

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Your package has been built on Linux, Mac, and Windows.

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[LiNk-NY]

Hi Yuzhu, @yduan004

Thank you for your submission to Bioconductor. Overall, your packages provide a lot of functionality and there is some conflation of software and experiment data packages within signatureSearchData.

Please see the review below for details.

If you have any questions, please post them as comments below.

Thank you. -Marcel

---

signatureSearch

• Do other packages provide an interface to the LINCS data and have you considered using them (see slinky)?

DESCRIPTION

• Looks good.
• Consider having org.Hs.eg.db in the Suggests field
• Date and Packaged fields are superfluous

NAMESPACE

• It looks like you're exporting a number S3 methods. What is the justification for using S3 over S4?
• Try to use a consistent case for all exported functions either snake_case or camelCase

vignettes

• The vignette looks pretty dense with text. Perhaps you want to reduce the amount of reading and provide a slim version of your paper here?
• You can point your users to the full paper if they would like to read it.
• Could you have saved the HDF5 files as SummarizedExperiments so that you don't have to write a function for it? (see HDF5Array::saveHDF5SummarizedExperiment)

R

• It seems that there is an implementation issue with the class as you are required to create all the methods again. I would look for an easier and smoother alternative that inherits from the data.frame class at least.
• query slot should be a list class instead of ANY. This will avoid unexpected behavior. You could also create a union class if you want to support more than one class. Ideally, you'd have some query type of class to provide in the qSig slot.
• Avoid using dontrun flags in the examples. Provide minimal examples that are easy to run and not computationally intense
• Avoid using loops in comp_fea_res. Create a list of tibbles and bind them after an lapply operation or use group_by and a function to run for each group. rbind(df, tb2) is not recommended.
• Avoid using eSet class. Please use the next gen, SummarizedExperiment class.
• Don't create methods for classes that are not your own as you're 'polluting' the other class's interface. Create a funnel type of function to handle different classes from the input and return the appropriate output for connectivity_score_raw etc.
• Avoid the use of @ to access class slots. Use dedicated accessor functions
• For functions with a lot of message calls, use a verbose argument for turning the messages on/off
• Use utils::globalVariables() to address NOTES
• Only use %>% and tidyverse / data.table if absolutely necessary in order to avoid unnecessary dependencies
• Data in extdata should not be accessed by gess_res_vis. Keep data that you'd like to use in a function in the data folder and invoke using data. Data in extdata is usually used for examples for a function that reads in a particular format
• Plotting functions should have open interfaces allowing your users to customize to their liking.

Minor

• Use c("geneRatio", "count") as the argument in the internal function
• Document errors for internal function as `stop(" ... ")
• Avoid the use of = assignment operator (for style)
• Avoid double logical evaluation (i.e., if (rerun == TRUE) and use if (rerun)

signatureSearchData

• The package should expose the data and not really provide extensive software functionality.
• For functions such as gctx2h5, they should go in a software package rather than the experiment data package.
• Why download data via FTP? The point of the experiment data package is to use AnnotationHub resources
• Many of these functions seem like utility functions and belong in an alternate package (a utils package of some sort). Analysis functions belong in the main package
• There should be no classes exported in the package
• Functions such as load_sqlite more often than not belong in the software package as unexported utility functions

vignettes

• In general, it looks like there is a lot of manual work involved in presenting these data objects to the user (e.g., affyid_annot chunk)
• The package should have a function to load the data object from HDF5 and present the user with a SummarizedExperiment. Users should not have to run readHDF5chunk themselves.

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