fix checking version text and finish sc integration

bcbio · Oct 11, 2024 · c1aa8fc · c1aa8fc
1 parent 1dad379
commit c1aa8fc
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Showing 11 changed files with 149 additions and 77 deletions.
diff --git a/inst/templates/base/reports/example.Rmd b/inst/templates/base/reports/example.Rmd
@@ -28,7 +28,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-stable-green) revision.

diff --git a/inst/templates/chipseq/QC/QC.Rmd b/inst/templates/chipseq/QC/QC.Rmd
@@ -33,7 +33,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-alpha-yellow) revision.

diff --git a/inst/templates/chipseq/diffbind/diffbind.Rmd b/inst/templates/chipseq/diffbind/diffbind.Rmd
@@ -41,7 +41,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-alpha-yellow) revision.

diff --git a/inst/templates/rnaseq/DE/Cross-comparison-analysis.Rmd b/inst/templates/rnaseq/DE/Cross-comparison-analysis.Rmd
@@ -28,8 +28,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
-stopifnot(compareVersion(package.version("Seurat"), "5.0.0")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-alpha-yellow) revision.

diff --git a/inst/templates/rnaseq/DE/DEG.Rmd b/inst/templates/rnaseq/DE/DEG.Rmd
@@ -42,7 +42,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-stable-green) revision.

diff --git a/inst/templates/rnaseq/DE/GSVA.Rmd b/inst/templates/rnaseq/DE/GSVA.Rmd
@@ -37,8 +37,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
-stopifnot(compareVersion(package.version("Seurat"), "5.0.0")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-alpha-yellow) revision.

diff --git a/inst/templates/rnaseq/DE/Intersections.Rmd b/inst/templates/rnaseq/DE/Intersections.Rmd
@@ -29,8 +29,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
-stopifnot(compareVersion(package.version("Seurat"), "5.0.0")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-alpha-yellow) revision.

diff --git a/inst/templates/rnaseq/QC/QC_nf-core.Rmd b/inst/templates/rnaseq/QC/QC_nf-core.Rmd
@@ -37,7 +37,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
 stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
-stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
 This code is in this ![](https://img.shields.io/badge/status-stable-green) revision.