diff --git a/R/pkg/R/utils.R b/R/pkg/R/utils.R
index ca8f8defdfdec..b9302585a03ce 100644
--- a/R/pkg/R/utils.R
+++ b/R/pkg/R/utils.R
@@ -546,6 +546,11 @@ processClosure <- function(node, oldEnv, defVars, checkedFuncs, newEnv) {
                        error = function(e) { FALSE })) {
             obj <- get(nodeChar, envir = func.env, inherits = FALSE)
             if (is.function(obj)) {
+              if (is.primitive(obj)) {
+                # Primitive functions have no closure to clean.
+                assign(nodeChar, obj, envir = newEnv)
+                break
+              }
               # If the node is a function call.
               funcList <- mget(nodeChar, envir = checkedFuncs, inherits = F,
                                ifnotfound = list(list(NULL)))[[1]]
@@ -592,7 +597,7 @@ processClosure <- function(node, oldEnv, defVars, checkedFuncs, newEnv) {
 # return value
 #   a new version of func that has a correct environment (closure).
 cleanClosure <- function(func, checkedFuncs = new.env()) {
-  if (is.function(func)) {
+  if (is.function(func) && !is.primitive(func)) {
     newEnv <- new.env(parent = .GlobalEnv)
     func.body <- body(func)
     oldEnv <- environment(func)
diff --git a/dev/infra/Dockerfile b/dev/infra/Dockerfile
index 83176aec80c53..d9c04eba9b266 100644
--- a/dev/infra/Dockerfile
+++ b/dev/infra/Dockerfile
@@ -19,7 +19,7 @@
 # See also in https://hub.docker.com/_/ubuntu
 FROM ubuntu:focal-20221019
 
-ENV FULL_REFRESH_DATE 20221118
+ENV FULL_REFRESH_DATE 20260510
 
 ENV DEBIAN_FRONTEND noninteractive
 ENV DEBCONF_NONINTERACTIVE_SEEN true
@@ -27,35 +27,31 @@ ENV DEBCONF_NONINTERACTIVE_SEEN true
 ARG APT_INSTALL="apt-get install --no-install-recommends -y"
 
 RUN apt-get clean
-RUN apt-get update
-RUN $APT_INSTALL software-properties-common git libxml2-dev pkg-config curl wget openjdk-8-jdk libpython3-dev python3-pip python3-setuptools python3.8 python3.9
+RUN apt-get update && $APT_INSTALL software-properties-common git libxml2-dev pkg-config curl wget openjdk-8-jdk libpython3-dev python3-pip python3-setuptools python3.8 python3.9
 RUN update-alternatives --set java /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
 
-RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.9
+RUN curl -sS https://bootstrap.pypa.io/pip/3.9/get-pip.py | python3.9
 
 RUN add-apt-repository ppa:pypy/ppa
-RUN apt update
-RUN $APT_INSTALL gfortran libopenblas-dev liblapack-dev
-RUN $APT_INSTALL build-essential
+RUN apt-get update && $APT_INSTALL gfortran libopenblas-dev liblapack-dev build-essential
 
 RUN mkdir -p /usr/local/pypy/pypy3.8 && \
     curl -sqL https://downloads.python.org/pypy/pypy3.8-v7.3.11-linux64.tar.bz2 | tar xjf - -C /usr/local/pypy/pypy3.8 --strip-components=1 && \
     ln -sf /usr/local/pypy/pypy3.8/bin/pypy /usr/local/bin/pypy3.8 && \
     ln -sf /usr/local/pypy/pypy3.8/bin/pypy /usr/local/bin/pypy3
 
-RUN curl -sS https://bootstrap.pypa.io/get-pip.py | pypy3
+RUN curl -sS https://bootstrap.pypa.io/pip/3.8/get-pip.py | pypy3
 
-RUN $APT_INSTALL gnupg ca-certificates pandoc
+RUN apt-get update && $APT_INSTALL gnupg ca-certificates pandoc
 RUN echo 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/' >> /etc/apt/sources.list
 RUN gpg --keyserver hkps://keyserver.ubuntu.com --recv-key E298A3A825C0D65DFD57CBB651716619E084DAB9
 RUN gpg -a --export E084DAB9 | apt-key add -
 RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
-RUN apt update
-RUN $APT_INSTALL r-base libcurl4-openssl-dev qpdf libssl-dev zlib1g-dev
+RUN apt-get update && $APT_INSTALL r-base libcurl4-openssl-dev qpdf libssl-dev zlib1g-dev libuv1-dev
 RUN Rscript -e "install.packages(c('remotes', 'knitr', 'markdown', 'rmarkdown', 'testthat', 'e1071', 'survival', 'arrow', 'roxygen2', 'xml2'), repos='https://cloud.r-project.org/')"
 
 # See more in SPARK-39959, roxygen2 < 7.2.1
-RUN apt-get install -y libcurl4-openssl-dev libgit2-dev libssl-dev libxml2-dev \
+RUN apt-get update && apt-get install -y libcurl4-openssl-dev libgit2-dev libssl-dev libxml2-dev \
           libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev \
           libtiff5-dev libjpeg-dev
 RUN Rscript -e "install.packages(c('remotes'), repos='https://cloud.r-project.org/')"
@@ -64,8 +60,11 @@ RUN Rscript -e "remotes::install_version('roxygen2', version='7.2.0', repos='htt
 # See more in SPARK-39735
 ENV R_LIBS_SITE "/usr/local/lib/R/site-library:${R_LIBS_SITE}:/usr/lib/R/library"
 
-RUN pypy3 -m pip install numpy 'pandas<=2.0.3' scipy coverage matplotlib
-RUN python3.9 -m pip install 'numpy==1.25.1' 'pyarrow==12.0.1' 'pandas<=2.0.3' scipy unittest-xml-reporting plotly>=4.8 'mlflow>=2.3.1' coverage 'matplotlib==3.7.2' openpyxl 'memory-profiler==0.60.0' 'scikit-learn==1.1.*'
+RUN printf 'beniget==0.4.1\npyproject-metadata==0.8.1\n' > /tmp/pypy-constraints.txt && \
+    PIP_CONSTRAINT=/tmp/pypy-constraints.txt pypy3 -m pip install numpy scipy coverage matplotlib && \
+    SETUPTOOLS_USE_DISTUTILS=stdlib pypy3 -m pip install 'pandas<=2.0.3' && \
+    rm /tmp/pypy-constraints.txt
+RUN python3.9 -m pip install 'numpy==1.25.1' 'pyarrow==12.0.1' 'pandas<=2.0.3' scipy unittest-xml-reporting 'plotly<6.0' 'mlflow>=2.3.1' coverage 'matplotlib==3.7.2' openpyxl 'memory-profiler==0.60.0' 'scikit-learn==1.1.*'
 
 # Add Python deps for Spark Connect.
 RUN python3.9 -m pip install 'grpcio>=1.48,<1.57' 'grpcio-status>=1.48,<1.57' 'protobuf==3.20.3' 'googleapis-common-protos==1.56.4'
diff --git a/python/mypy.ini b/python/mypy.ini
index 3443af9a86503..44d3f73e4da53 100644
--- a/python/mypy.ini
+++ b/python/mypy.ini
@@ -169,3 +169,9 @@ ignore_missing_imports = True
 ; Ignore errors for proto generated code
 [mypy-pyspark.sql.connect.proto.*, pyspark.sql.connect.proto]
 ignore_errors = True
+
+[mypy-pydantic.*]
+follow_imports = skip
+
+[mypy-sqlalchemy.*]
+follow_imports = skip