alabaster.sfe

[lambdamoses]

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• Repository: https://github.com/pachterlab/alabaster.sfe

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[bioc-issue-bot]

Hi @lambdamoses

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: alabaster.sfe
Type: Package
Title: Language agnostic on disk serialization of SpatialFeatureExperiment
Version: 0.99.0
Authors@R: 
    person("Lambda", "Moses", email = "[email protected]", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-7092-9427"))
Description: 
    Builds upon the existing ArtifactDB project, expending alabaster.spatial for
    language agnostic on disk serialization of SpatialFeatureExperiment.
Depends: 
    SpatialFeatureExperiment (>= 1.9.3),
    alabaster.base
Imports:
    alabaster.sce,
    alabaster.spatial (>= 1.5.2),
    EBImage,
    jsonlite,
    methods,
    RBioFormats,
    S4Vectors,
    sfarrow,
    SingleCellExperiment,
    spdep,
    SummarizedExperiment,
    terra,
    xml2
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Suggests: 
    BiocStyle,
    fs,
    knitr,
    rmarkdown,
    scater,
    sf,
    SFEData,
    testthat (>= 3.0.0),
    Voyager (>= 1.9.1)
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://pachterlab.github.io/alabaster.sfe/
biocViews:
    DataRepresentation,
    Spatial

[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.

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

[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): alabaster.sfe_0.99.0.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/alabaster.sfe to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lambdamoses]

Here's the error from BiocCheck, which I can't do anything about:

ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.

[lshep]

Are you registered on the support site with that email?

[lambdamoses]

OK, I found that I haven't changed my email on the support site. I have changed it just now.

[lshep]

can you please do another version bump to trigger a new build report

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d9ce7a7ab07de68c690aca15c05b184b42fac228

[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): alabaster.sfe_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/alabaster.sfe to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[vjcitn]

Hi, I'll probably be reviewing this. I just did a build/check in the devel container and hit

> d <- VizgenOutput(dataset = "cellpose", file_path = fn)
Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead
Warning: Could not check database for updates.
  Database source currently unreachable.
  This should only be a temporary interruption. 
  Using previously cached version.
Error in value[[3L]](cond) : failed to connect
  reason: Couldn't resolve host name [bioconductor.org]: GnuTLS recv error (-110): The TLS connection was non-properly terminated.
  Consider rerunning with 'localHub=TRUE'
Calls: VizgenOutput ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    reason: Couldn't resolve host name [bioconductor.org]: Could not resolve host: bioconductor.org
    Consider rerunning with 'localHub=TRUE'
  Backtrace:
      ▆
   1. └─SFEData::VizgenOutput(dataset = "cellpose", file_path = fn) at test.R:11:1
   2.   └─ExperimentHub::ExperimentHub()
   3.     └─AnnotationHub::.Hub(...)

can tests be robust to this? It might be a pretty artificial situation but worth considering. Also please
check the timing event reported in the log above.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 4249dec1a60281a6ecf96f8d3f1aa6b4edb88466

[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): alabaster.sfe_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/alabaster.sfe to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.