bump version

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: sctransform
 Type: Package
 Title: Variance Stabilizing Transformations for Single Cell UMI Data
-Version: 0.3.5.9007
+Version: 0.4.0
 Date: 2023-09-18
 Authors@R: c(
   person(given = "Christoph", family = "Hafemeister", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-6365-8254")),
@@ -20,7 +20,7 @@ BugReports: https://github.com/satijalab/sctransform/issues
 License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-Depends: R (>= 3.5.0)
+Depends: R (>= 3.6.0)
 LinkingTo: RcppArmadillo, Rcpp (>= 0.11.0)
 SystemRequirements: C++17
 Imports:

NEWS.md

@@ -1,7 +1,7 @@
 # News
 All notable changes will be documented in this file.
 
-## Unreleased
+## [0.5.0] - 2023-09-18
 
 ### Added
 - Add `fit_nb_offset` to support vst.flavor='v2' by default

inst/CITATION

@@ -1,8 +1,10 @@
 citHeader("To cite sctransform in publications, please use:")
 
-citEntry(entry = "article",
-  author = personList(as.person("Christoph Hafemeister"),
-                      as.person("Rahul Satija")),
+bibentry(bibtype = "article",
+  author = c(person(given = "Christoph", family = "Hafemeister", email = "[email protected]", role = "aut",
+  comment = c(ORCID = "0000-0001-6365-8254")),
+  person(given = "Rahul", family = "Satija", email = "[email protected]", role = c("aut", "ctb"), comment = c(ORCID = "000
+  -0001-9448-8833"))),
   title = "Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression",
   journal = "Genome Biology",
   year = "2019",
@@ -13,9 +15,9 @@ citEntry(entry = "article",
   textVersion = "Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol 20, 296 (2019)."
 )
 
-citEntry(entry = "article",
-  author = personList(as.person("Saket Choudhary"),
-                      as.person("Rahul Satija")),
+bibentry(bibtype = "article",
+  author = c(person(given = "Saket", family = "Choudhary", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = "Rahul", family = "Satija", email = "[email protected]", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-9448-8833"))),
   title = "Comparison and evaluation of statistical error models for scRNA-seq",
   journal = "Genome Biology",
   year = "2022",

revdep/README.md

@@ -1,63 +1,49 @@
 # Platform
 
-|field    |value                        |
-|:--------|:----------------------------|
-|version  |R version 4.0.0 (2020-04-24) |
-|os       |Ubuntu 18.04.6 LTS           |
-|system   |x86_64, linux-gnu            |
-|ui       |RStudio                      |
-|language |(EN)                         |
-|collate  |en_US.UTF-8                  |
-|ctype    |en_US.UTF-8                  |
-|tz       |America/New_York             |
-|date     |2022-01-10                   |
+|field    |value                                          |
+|:--------|:----------------------------------------------|
+|version  |R version 4.3.1 (2023-06-16)                   |
+|os       |Ubuntu 20.04.6 LTS                             |
+|system   |x86_64, linux-gnu                              |
+|ui       |RStudio                                        |
+|language |(EN)                                           |
+|collate  |en_US.UTF-8                                    |
+|ctype    |en_US.UTF-8                                    |
+|tz       |America/New_York                               |
+|date     |2023-09-18                                     |
+|rstudio  |2023.03.1+446 Cherry Blossom (server)          |
+|pandoc   |3.1.3 @ /home/choudharys/miniconda3/bin/pandoc |
 
 # Dependencies
 
-|package       |old        |new        |Δ  |
-|:-------------|:----------|:----------|:--|
-|sctransform   |0.3.2      |0.3.3      |*  |
-|cli           |NA         |3.1.0      |*  |
-|colorspace    |NA         |2.0-2      |*  |
-|crayon        |NA         |1.4.2      |*  |
-|digest        |NA         |0.6.29     |*  |
-|dplyr         |NA         |1.0.7      |*  |
-|ellipsis      |NA         |0.3.2      |*  |
-|fansi         |NA         |1.0.0      |*  |
-|farver        |NA         |2.1.0      |*  |
-|future        |NA         |1.23.0     |*  |
-|future.apply  |NA         |1.8.1      |*  |
-|generics      |NA         |0.1.1      |*  |
-|ggplot2       |NA         |3.3.5      |*  |
-|globals       |NA         |0.14.0     |*  |
-|glue          |NA         |1.6.0      |*  |
-|isoband       |NA         |0.2.5      |*  |
-|labeling      |NA         |0.4.2      |*  |
-|lifecycle     |NA         |1.0.1      |*  |
-|magrittr      |NA         |2.0.1      |*  |
-|matrixStats   |0.61.0     |0.61.0     |   |
-|parallelly    |NA         |1.30.0     |*  |
-|pillar        |NA         |1.6.4      |*  |
-|R6            |NA         |2.5.1      |*  |
-|Rcpp          |NA         |1.0.7      |*  |
-|RcppArmadillo |0.10.7.5.0 |0.10.7.5.0 |   |
-|rlang         |NA         |0.4.12     |*  |
-|scales        |NA         |1.1.1      |*  |
-|stringi       |NA         |1.7.6      |*  |
-|tibble        |NA         |3.1.6      |*  |
-|tidyselect    |NA         |1.1.1      |*  |
-|utf8          |NA         |1.2.2      |*  |
-|vctrs         |NA         |0.3.8      |*  |
-|viridisLite   |NA         |0.4.0      |*  |
-|withr         |NA         |2.4.3      |*  |
+|package       |old   |new        |Δ  |
+|:-------------|:-----|:----------|:--|
+|sctransform   |0.3.5 |0.4.0      |*  |
+|digest        |NA    |0.6.33     |*  |
+|dplyr         |NA    |1.1.3      |*  |
+|future        |NA    |1.33.0     |*  |
+|future.apply  |NA    |1.11.0     |*  |
+|ggplot2       |NA    |3.4.3      |*  |
+|gtable        |NA    |0.3.4      |*  |
+|labeling      |NA    |0.4.3      |*  |
+|matrixStats   |NA    |1.0.0      |*  |
+|parallelly    |NA    |1.36.0     |*  |
+|Rcpp          |NA    |1.0.11     |*  |
+|RcppArmadillo |NA    |0.12.6.4.0 |*  |
+|rlang         |NA    |1.1.1      |*  |
+|vctrs         |NA    |0.6.3      |*  |
+|viridisLite   |NA    |0.4.2      |*  |
 
 # Revdeps
 
-## Failed to check (3)
+## Failed to check (6)
 
 |package |version |error |warning |note |
 |:-------|:-------|:-----|:-------|:----|
 |CAMML   |?       |      |        |     |
+|EWCE    |?       |      |        |     |
 |muscat  |?       |      |        |     |
+|RESET   |?       |      |        |     |
 |Seurat  |?       |      |        |     |
+|VAM     |?       |      |        |     |
 

revdep/cran.md

@@ -1,6 +1,6 @@
 ## revdepcheck results
 
-We checked 4 reverse dependencies (1 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 6 reverse dependencies (0 from CRAN + 6 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
  * We failed to check 0 packages

revdep/failures.md

@@ -30,6 +30,39 @@
 
 
 
+```
+# EWCE
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/satijalab/sctransform
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
 ```
 # muscat
 
@@ -63,6 +96,39 @@
 
 
 
+```
+# RESET
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/satijalab/sctransform
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
 ```
 # Seurat
 
@@ -96,4 +162,37 @@
 
 
 
+```
+# VAM
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/satijalab/sctransform
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
 ```