R SIG Debian - Jun 2022 - Trying to install r-stan without using rocker

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]]

Jesse,

On 13 June 2022 at 12:19, Jesse McMullen-Crummey wrote:
| 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.

If something does not work, I usually backtrack.

You start from python:3.8-slim-bullseye. That is your right. But this is a
Debian-and-R mailing list, so we may not have started from there.

I maintain and curate several sets of Rocker containers building either on
 - plain Debian as our rocker/r-base which is also the official r-base
 - Ubuntu because I can then use Ubuntu binaries as from c2d4u or now also r2u

If I were, I'd the same. With either base set you should get to 'apt
install r-cran-rstan'
easily, and adding your other package is easy. (If you look at work I worked
on recently via its site https://eddelbuettel.github.io/r2u/ you will see
that staring from eg eddelbuettel/r2u:22.04 you can run a single
   Rscript -e 'install.packages(c("rstan", "stringr",
"gtools", "tidyr"))'
without issues giving your the R side to which you can then add your Python
requirements. I usually try that first interactively in the same Docker
container.

If all that fails, maybe you want to emphasize Python first and use Anaconda
via mamba. Some folks had good luck with that (but don't mix and match, only
tears result from that).  We cannot help with *conda here.

Dirk


| 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]]
| 
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-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org