Merge pull request #92 from AlexsLemonade/jashapiro/update-R

Update R, Bioconductor, and anndata to the current versions
AlexsLemonade · Aug 17, 2022 · 7dac599 · 7dac599
2 parents 6d821f1 + 81fe41b
commit 7dac599
Show file tree

Hide file tree

Showing 6 changed files with 327 additions and 314 deletions.
diff --git a/envs/scanorama.yaml b/envs/scanorama.yaml
@@ -6,7 +6,7 @@ channels:
 dependencies:
   - python=3.9
   - scanorama=1.7.1
-  - anndata=0.7.6
+  - anndata=0.8.0
   - ca-certificates
   - openssl
   - git

diff --git a/envs/scpca-renv.post-deploy.sh b/envs/scpca-renv.post-deploy.sh
@@ -15,6 +15,7 @@ fi
 
 
 
-
+# install packages required for renv
+Rscript --no-init-file -e 'install.packages(c("jsonlite","purrr"), repos = "https://cloud.r-project.org")'
 # restore packages
 Rscript -e 'renv::restore()'
diff --git a/envs/scpca-renv.yaml b/envs/scpca-renv.yaml
@@ -8,6 +8,4 @@ dependencies:
   - pandoc
   - pkg-config
   - openssl
-  - r-base=4.1.3
-  - r-jsonlite
-  - r-purrr
+  - r-base=4.2.1
diff --git a/envs/scvi.yaml b/envs/scvi.yaml
@@ -4,5 +4,6 @@ channels:
   - bioconda
   - defaults
 dependencies:
+  - anndata=0.8.0
   - scvi-tools=0.17.1
   - gitpython