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Merge pull request #8484 from satijalab/release/5.0.2
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Prep for release of 5.0.2
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dcollins15 authored Feb 28, 2024
2 parents 6a3ef5e + dd4d754 commit 2b9ee19
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: Seurat
Version: 5.0.1.9009
Date: 2024-02-26
Version: 5.0.2
Date: 2024-02-28
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Authors@R: c(
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2 changes: 1 addition & 1 deletion NEWS.md
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# Unreleased
# Seurat 5.0.2 (2024-02-28)

## Changes

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63 changes: 6 additions & 57 deletions cran-comments.md
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# Seurat v5.0.0
# Seurat v5.0.2

## Test environments
* local ubuntu 20.04 install, R 4.1.3
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There were no ERRORs or WARNINGs

There were two NOTEs

> * checking CRAN incoming feasibility ... NOTE
> Maintainer: 'Rahul Satija <[email protected]>'
> New maintainer:
> Rahul Satija <[email protected]>
> Old maintainer(s):
> Paul Hoffman <[email protected]>
New maintainer is Rahul Satija, the email address has remained the same.
There was one NOTE

> Suggests or Enhances not in mainstream repositories:
> BPCells, presto
> Availability using Additional_repositories specification:
> presto yes https://satijalab.r-universe.dev
> BPCells no ?
> ? ? https://bnprks.r-universe.dev
> Additional repositories with no packages:
> https://bnprks.r-universe.dev
> Packages suggested but not available for checking: 'BPCells', 'presto'
> BPCells yes https://satijalab.r-universe.dev
BPCells and presto are hosted on R-universe and used conditionally in Seurat.


## Downstream dependencies

The following reverse dependencies are impacted by this release of Seurat:

- AnanseSeurat
- Failure in examples and test because of changes in how default objects are created in Seurat.
- Functionality impacted. The author was made aware of these changes: https://github.com/JGASmits/AnanseSeurat/issues/34

- CAMML
- Failure in example because of changes in how default objects are created in Seurat.
- Functionality impacted. The author was made aware of these changes over email

- Canek
- Failure in tests because of changes in how default objects are created in Seurat.
- Functionality impacted. The author was made aware of these changes: https://github.com/MartinLoza/Canek/issues/20

- clustree:
- Failure in tests because of changes in data accessor methods in Seurat.
- Functionality impacted. The author was made aware of these changes: https://github.com/lazappi/clustree/issues/93
- Author has incorporated changes

- CSCDRNA
- Failure in tests because of changes in data accessor methods in Seurat.
- Functionality impacted. The author was made aware of these changes: https://github.com/empiricalbayes/CSCDRNA/issues/1

- scCustomize
- Failure in example because of changes in how default objects are created in Seurat.
- Functionality impacted. The author was made aware of these changes: https://github.com/samuel-marsh/scCustomize/issues/131

- SCpubr:
- Failure in example because of changes in how default objects are created in Seurat.
- Functionality impacted. The author was made aware of these changes: https://github.com/enblacar/SCpubr/issues/42
There are two packages that depend on Seurat: CACIMAR and scCustomize; this update does not impact their functionality

- Signac
- Faulure in new tests because of SeuratObject changing the order of the results, but not the actual values.
- Functionality not impacted. The author was made aware of these changes over email and has made changes.
There are 28 packages that import Seurat: AnanseSeurat, APackOfTheClones, bbknnR, CAMML, DR.SC, DWLS, ggsector, mixhvg, nebula, Platypus, PRECAST, ProFAST, rPanglaoDB, scaper, scDiffCom, scfetch, scGate, scGOclust, scMappR, scperturbR, scpoisson, SCRIP, scRNAstat, SignacX, SoupX, SPECK, STREAK, and tidyseurat; this update does not impact their functionality

- tidyseurat
- Faulure in new tests because of SeuratObject changing the order of the results, but not the actual values.
- Functionality not impacted. The author was made aware of these changes: https://github.com/stemangiola/tidyseurat/issues/74
- VAM
- Failure in tests because of changes in data accessor methods in Seurat.
- Functionality impacted. The author was made aware of these changes over email
There are 22 packages that suggest Seurat: BisqueRNA, Canek, cellpypes, CIARA, ClustAssess, clustree, combiroc, conos, countland, CRMetrics, CytoSimplex, DIscBIO, dyngen, grandR, harmony, RESET, rliger, SCORPIUS, SCpubr, Signac, treefit, and VAM; this update does not impact their functionality
15 changes: 10 additions & 5 deletions tests/testthat/test_integration5.R
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Expand Up @@ -93,7 +93,9 @@ test_that("IntegrateLayers works with CCAIntegration", {
)
expect_abs_equal(
Embeddings(integrated[["integrated"]])[75, 45],
0.544193
0.544193,
# added to pass macOS builder checks for v5.0.2
tolerance = 8.1e-06
)
})

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)
expect_abs_equal(
Embeddings(integrated[["integrated"]])[75, 45],
0.544193
0.544193,
# added to pass macOS builder checks for v5.0.2
tolerance = 8.1e-06
)
})

Expand Down Expand Up @@ -153,12 +157,13 @@ test_that("IntegrateLayers works with JointPCAIntegration", {
)
expect_abs_equal(
Embeddings(integrated[["integrated"]])[40, 25],
0.324614,
tolerance = 1.0e-6
0.324614
)
expect_abs_equal(
Embeddings(integrated[["integrated"]])[75, 45],
0.544193
0.544193,
# added to pass macOS builder checks for v5.0.2
tolerance = 8.1e-06
)
})

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