Contributions
Contributions copied to clipboard
Bioconductor
smoppix
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/sthawinke/smoppix
Confirm the following by editing each check box to '[x]'
-
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
-
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
-
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
-
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
-
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
-
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
-
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
- [x] The 'devel' branch for new packages and features.
- [x] The stable 'release' branch, made available every six months, for bug fixes.
- [x] Bioconductor version control using Git (optionally via GitHub).
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.
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 = "[email protected]",
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
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.
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
I have added an introduction to the vignette, and compressed the data files
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.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.
Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account
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
[email protected]:packages/smoppix 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: 233f9a08d03d59f1afc15f876ce67f0b03d403d0
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
[email protected]:packages/smoppix 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: 49a019f8445772232a614a99702d8680901f438e
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
[email protected]:packages/smoppix to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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
Received a valid push on git.bioconductor.org; starting a build for commit id: 98a065f85fa21d8d08f2a4a501ae0000ee33eb63
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
[email protected]:packages/smoppix 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: 1fb93897349a6d579c5d0011afce3e73b168e135
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
[email protected]:packages/smoppix 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: ebc3a6f2621e3841a2fd6eb3388ca16c905e6e03
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
[email protected]:packages/smoppix 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: aa0f6c0f029a7d3477d253543cddba156cb3082f
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, 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_0.99.9.tar.gz macOS 12.7.1 Monterey: smoppix_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
[email protected]:packages/smoppix 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: 6dca66acaf4ec36c4c451df09ad6cef678f8f8c1
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, 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: macOS 12.7.1 Monterey: smoppix_0.99.11.tar.gz Linux (Ubuntu 22.04.3 LTS): smoppix_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
[email protected]:packages/smoppix 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: b86b8f34c0334706a328d8eda59ef108970565a8
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: macOS 12.7.1 Monterey: smoppix_0.99.12.tar.gz Linux (Ubuntu 22.04.3 LTS): smoppix_0.99.12.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/smoppix 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: 8bfa96ce57ab0944dd051618e7dc35894fd084e8
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: macOS 12.7.1 Monterey: smoppix_0.99.13.tar.gz Linux (Ubuntu 22.04.3 LTS): smoppix_0.99.13.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/smoppix to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@ococrook I do not understand this warning
Package listed as VignetteEngine or VignetteBuilder but not currently Suggested.
Both the knitr and rmarkdown packages are in the suggested list. This warning seems to have come up with the latest BiocCheck version, although I cannot reproduce it locally, or find anything on this online. Could this be a bug?
@sthawinke I've asked @LiNk-NY for clarification about this warning in another current package review (https://github.com/Bioconductor/Contributions/issues/3451#issuecomment-2246375041)
@sthawinke
It is safe to ignore. It was a false positive. It should be fixed in BiocCheck version 1.41.7.
Received a valid push on git.bioconductor.org; starting a build for commit id: b1b82b19d56edfb14c2a63c16dfbec9fe0e5ae7d