smoppix

[sthawinke]

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[bioc-issue-bot]

Hi @sthawinke

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: smoppix
Type: Package
Title: Analyze Single Molecule Spatial Transcriptomics and Other Spatial Omics Data Using the Probabilistic Index
Version: 0.99.0
Authors@R: 
    c(person(given = "Stijn", family = "Hawinkel", 
    email = "stijn.hawinkel@psb.ugent.be", 
    role=c("cre", "aut"), comment = c(ORCID = "0000-0002-4501-5180")))
Description: Test for univariate and multivariate spatial patterns in 
    spatial omics data with single-molecule resolution. The tests implemented 
    allow for analysis of nested designs and are automatically calibrated to different
    biological specimens. Tests for aggregation, colocalization, gradients and vicinity to cell edge or centroid are provided.
License: GPL-2
Encoding: UTF-8
Imports: spatstat.geom(>= 3.2.0),spatstat.random, methods,BiocParallel,SummarizedExperiment,SpatialExperiment,scam,Rdpack,stats,utils,extraDistr,lmerTest,lme4,ggplot2,graphics,grDevices,Rcpp (>= 1.0.11),Matrix,spatstat.model,openxlsx
Suggests: testthat,rmarkdown,knitr,DropletUtils,polyCub,RImageJROI,sp,ape
RdMacros: Rdpack
RoxygenNote: 7.3.1
biocViews: Transcriptomics, Spatial, SingleCell
Depends: R (>= 4.3.0)
VignetteBuilder: knitr
BugReports: https://github.com/sthawinke/smoppix
URL: https://github.com/sthawinke/smoppix
LinkingTo: Rcpp

[lshep]

Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope.

[lshep]

You should also fix the following from R CMD check

* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
             old_size new_size compress
  Eng.RData     2.2Mb    1.9Mb       xz
  Yang.RData    936Kb    422Kb       xz

[sthawinke]

I have added an introduction to the vignette, and compressed the data files

[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
assigned or provide a justification on why you feel the ERROR or
WARNING should be granted an exception.

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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 22.04.3 LTS): smoppix_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/smoppix 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: 233f9a08d03d59f1afc15f876ce67f0b03d403d0

[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 22.04.3 LTS): smoppix_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/smoppix 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: 49a019f8445772232a614a99702d8680901f438e

[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: "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 Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): smoppix_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/smoppix to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[sthawinke]

I am getting the warning

"Checking for Bioconductor software dependencies...
* WARNING: No Bioconductor dependencies detected. Reach out to the
Bioconductor community or consider a CRAN submission."

Yet the package does import BiocParallel, SummarizedExperiment and SpatialExperiment which are all BioConductor software packages, so I don't understand where this comes from

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 98a065f85fa21d8d08f2a4a501ae0000ee33eb63

[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 22.04.3 LTS): smoppix_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/smoppix 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: 1fb93897349a6d579c5d0011afce3e73b168e135

[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 22.04.3 LTS): smoppix_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/smoppix 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: ebc3a6f2621e3841a2fd6eb3388ca16c905e6e03

[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 22.04.3 LTS): smoppix_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/smoppix 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.