Hi All,
I found your mailing list via a stack overflow mention. I’m currently on my
second full day of trying to build a docker container to use as an AWS lambda
fcn and am feeling pretty stuck - I was hoping someone here could help. It
needs to support python+R+rstan.
I currently construct the docker image from a python/debian base image. I can
get R working fine, but when I try to run an r-stan script within the lambda
function I get a ’there is no package called Stan”, despite a good 5 minutes of
the image build being dedicated to the download of rstan. Am looking for
advice here on how to proceed. My current dockerfile follows…
################
FROM python:3.8-slim-bullseye
ENV DEBIAN_FRONTEND=noninteractive
ENV LC_ALL=C.UTF-8
ENV LANG=en_US.UTF-8
ENV TZ=:/etc/localtime
ENV PATH=/var/lang/bin:/usr/local/bin:/usr/bin/:/bin:/opt/bin
ENV
LD_LIBRARY_PATH=/var/lang/lib:/lib64:/usr/lib64:/var/runtime:/var/runtime/lib:/var/task:/var/task/lib:/opt/lib
ENV LAMBDA_TASK_ROOT=/var/task
ENV LAMBDA_RUNTIME_DIR=/var/runtime
# Define custom function directory
ARG FUNCTION_DIR="/var/task"
WORKDIR ${FUNCTION_DIR}
# Install aws-lambda-cpp build dependencies + r
RUN apt-get update && \
apt-get install -y \
g++ \
make \
cmake \
unzip \
libcurl4-openssl-dev \
r-base
COPY requirements.txt .
COPY irt_dim_red.R .
COPY . .
#install the python requirements
RUN pip install -r requirements.txt
COPY scripts/install_stan.R install_stan.R
RUN Rscript "install_stan.R"
RUN R -e "install.packages('stringr')"
RUN R -e "install.packages('gtools')"
RUN R -e "install.packages('tidyr')"
# Set the CMD to your handler (could also be done as a parameter override
outside of the Dockerfile)
ENTRYPOINT [ "/usr/local/bin/python", "-m", "awslambdaric" ]
CMD [ "main.handler"]
Where the script install_rstan.R is:
# Following instructions from
# https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Linux
print("Running install_stan.R")
## Creating /home/rstudio/.R/Makevars
dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (!file.exists(M)) file.create(M)
cat("\nCXX14FLAGS=-O3 -march=native -mtune=native -fPIC",
"CXX14=clang++",
file = M, sep = "\n", append = TRUE)
## Installing rstan
install.packages("rstan", dependencies=TRUE, type = "source")
Any help would be massively appreciated.
Jesse
—
Jesse McMullen-Crummey, PhD (he/him)
Data Engineer
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
