wSIR

[shazanfar]

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• Repository: https://github.com/SydneyBioX/wSIR

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[bioc-issue-bot]

Hi @shazanfar

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: wSIR
Type: Package
Title: Weighted Sliced Inverse Regression (wSIR) for supervised
        dimension reduction of spatial transcriptomics and single cell
        gene expression data
Version: 0.99.0
Authors@R: c(
    person("Max", "Woollard", email = "[email protected]", 
    role = c("aut", "cre", "ctb"),
    comment=c(ORCID="0009-0000-6319-6926")),
    person("Pratibha", "Panwar", role = c("ctb"), 
    comment = c(ORCID = "0000-0002-7437-7084")),
    person("Linh", "Nghiem", role = c("aut","ctb"),
    comment=c(ORCID = "0000-0003-2874-9067")),
    person("Shila", "Ghazanfar", email = "[email protected]", 
    role = c("aut", "ctb"), comment=c(ORCID="0000-0001-7861-6997"))
    )
Description: Weighted Sliced Inverse Regression (wSIR) is a supervised dimension 
    reduction algorithm for spatial transcriptomics gene expression data. For a 
    provided gene expression matrix and dataframe of each cell's spatial 
    coordinates, wSIR creates a low-dimensional representation of the gene 
    expression data that preserves the ability to predict spatial coordinates 
    that was present in the gene expression data. Furthermore, wSIR provides 
    interpretable loadings which allow for projection of new single-cell gene 
    expression data into a low-dimensional space which preserves the spatial 
    information present in the gene expression data.
License: GPL-2
Encoding: UTF-8
URL: https://sydneybiox.github.io/wSIR
BugReports: https://github.com/sydneybiox/wSIR/issues
biocViews: DimensionReduction,
    Software,
    GeneExpression, 
    SingleCell,
    Spatial,
    Transcriptomics,
    Regression
LazyData: false
Roxygen: list(markdown = TRUE)
Depends: R (>= 4.4.0),
Imports: Rfast,
    magrittr,
    ggplot2,
    umap,
    vctrs,
    stringr,
    distances,
    Rcpp (>= 1.0.11),
    doBy,
    BiocParallel,
    rlang,
    methods
Suggests: knitr,
    BiocStyle,
    class
LinkingTo: Rcpp,
    RcppArmadillo
VignetteBuilder: knitr
RoxygenNote: 7.3.2
NeedsCompilation: yes
Packaged: 2024-08-19 05:25:13 UTC; linhnghiem

[lshep]

We like to see interoperability with standard Bioconductor class structures; This package should be expanded to also work with SpatialExperiment or SingleCellExperiment Bioconductor class structures.

[shazanfar]

Hi @lshep we have now added interoperability with the SpatialExperiment and SingleCellExperiment via the runwSIR and calculatewSIR functions, also added BiocParallel use in the exploreWSIRParams function. Thanks, Shila

[lshep]

I'm getting the following ERROR when trying to build locally:

R CMD build wSIR 
* checking for file 'wSIR/DESCRIPTION' ... OK
* preparing 'wSIR':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package 'wSIR' ...
** using staged installation
** libs
using C++ compiler: 'g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
g++ -std=gnu++17 -I"/home/lorikern/R-Installs/bin/R-4-4-branch/include" -DNDEBUG  -I'/home/lorikern/R-Libraries/R4.4-Bioc3.20/Rcpp/include' -I'/home/lorikern/R-Libraries/R4.4-Bioc3.20/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/lorikern/R-Installs/bin/R-4-4-branch/include" -DNDEBUG  -I'/home/lorikern/R-Libraries/R4.4-Bioc3.20/Rcpp/include' -I'/home/lorikern/R-Libraries/R4.4-Bioc3.20/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2   -c matrixmult.cpp -o matrixmult.o
g++ -std=gnu++17 -shared -L/home/lorikern/R-Installs/bin/R-4-4-branch/lib -L/usr/local/lib -o wSIR.so RcppExports.o matrixmult.o -L/home/lorikern/R-Installs/bin/R-4-4-branch/lib -lR
installing to /tmp/RtmpfvydgC/Rinst6b6c471bf667/00LOCK-wSIR/00new/wSIR/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'wSIR' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/tmp/RtmpfvydgC/Rinst6b6c471bf667/00LOCK-wSIR/00new/wSIR/libs/wSIR.so':
  /tmp/RtmpfvydgC/Rinst6b6c471bf667/00LOCK-wSIR/00new/wSIR/libs/wSIR.so: undefined symbol: dorgqr_
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/tmp/RtmpfvydgC/Rinst6b6c471bf667/wSIR'
      -----------------------------------
ERROR: package installation failed

[shazanfar]

Hi @lshep we have made changes that I believe means you should be able to build now, do you mind trying again and letting us know how it goes? Thanks, Shila

[bioc-issue-bot]

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
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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 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 24.04.1 LTS): wSIR_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
[email protected]:packages/wSIR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9091581a743e92c3f91b3e9177911906a710dec7

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): wSIR_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
[email protected]:packages/wSIR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.