force reticulate pandas and numpy version to be stable versions

Author: rxu17

Dockerfile

@@ -16,14 +16,6 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
 RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
 
-# Add CRAN repo and key for R
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    dirmngr gnupg curl software-properties-common ca-certificates
-
-RUN curl -fsSL https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | gpg --dearmor -o /usr/share/keyrings/cran-archive-keyring.gpg && \
-    echo "deb [signed-by=/usr/share/keyrings/cran-archive-keyring.gpg] https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" \
-    > /etc/apt/sources.list.d/cran-r.list
-
 # General sys dependencies
 RUN apt-get update && apt-get install -y --allow-unauthenticated --no-install-recommends \
 		bedtools \

R/install_packages.R

@@ -8,3 +8,5 @@ library(testthat)
 library(VariantAnnotation)
 library(xtable)
 library(ggpubr)
+library(reticulate)
+reticulate::py_install(c("pandas>=1.5,<=2.0.3", "numpy<=1.24.4"))

requirements.txt

@@ -6,3 +6,4 @@ pyranges==0.1.4
 # known working version 6.0
 PyYAML>=5.1
 synapseclient[pandas]>=4.0.0, <5.0.0
+opentelemetry-semantic-conventions==0.56b0