sysreqs::sysreqs() != eval sysreqs::sysreq_commands() on rocker/rstudio:3.6.2 (and others?)

[maxheld83]

This installs zlib (a dependency of, among other things {data.table}) as expected with docker build --no-cache -t reprex .:

Dockerfile:

# works
FROM rhub/debian-gcc-release
# does not work
# FROM rocker/rstudio:3.6.2

RUN echo "Imports: data.table" > DESCRIPTION

RUN Rscript -e "options(warn = 2); install.packages('remotes')"
RUN Rscript -e "options(warn = 2); remotes::install_github('r-hub/sysreqs')"
RUN Rscript -e "options(warn = 2); sysreqs::sysreq_commands(desc = 'DESCRIPTION', platform = 'linux-x86_64-debian-gcc')"
# next line is actually the output of above line
# but must be added manually, otherwise zlib is not installed, or at least headers are not found
# RUN export DEBIAN_FRONTEND=noninteractive; apt-get -y update && apt-get install -y  zlib1g-dev
RUN Rscript -e "options(warn = 2); sysreqs::sysreqs(desc = 'DESCRIPTION', platform = 'linux-x86_64-debian-gcc')"
RUN Rscript -e "options(warn = 2); install.packages('data.table')"

however, this fails for FROM rocker/rstudio:3.6.2, which AFAIK, is debian-gcc:

fwrite.c:10:10: fatal error: zlib.h: No such file or directory
 #include <zlib.h>      // for compression to .gz
          ^~~~~~~~
compilation terminated.
make: *** [/usr/local/lib/R/etc/Makeconf:168: fwrite.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/usr/local/lib/R/site-library/data.table’
Error in install.packages("data.table") :
  (converted from warning) installation of package ‘data.table’ had non-zero exit status
Execution halted

Weirder still, the problem can be solved by manually installing zlib with

RUN export DEBIAN_FRONTEND=noninteractive; apt-get -y update && apt-get install -y  zlib1g-dev

which is the exact command which, according to sysreqs::sysreq_commands(), sysreqs::sysreqs() is running.
So that makes me think that the sysreqsdb entry is fine here, but something weird is going on with sysreqs::sysreqs().

Also paging @nuest who might have run into similar issues in containerit and @Robinlovelace who reported a similar issue in rocker-org/rocker-versioned#201.

[maxheld83]

using @jimhester's "hack" (?) from the tidverse github actions also solves the problem, though I have no idea why:

Dockerfile:

FROM rocker/rstudio:3.6.2

RUN echo "Imports: data.table" > DESCRIPTION

# install system dependencies
RUN Rscript -e "options(warn = 2); install.packages('remotes')"
RUN Rscript -e "options(warn = 2); remotes::install_github('r-hub/sysreqs')"
ENV RHUB_PLATFORM="linux-x86_64-debian-gcc"
RUN sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") && \
    eval "$sysreqs"

# install dependencies
RUN Rscript -e "options(warn = 2); install.packages('data.table')"

[gaborcsardi]

sysreqs does not detect the platform, just uses the one set in the RHUB_PLATFORM environment variable.

[maxheld83]

yes, sorry, that wasn't my problem here.
I understand that I can either set RHUB_PLATFORM or platform = 'linux-x86_64-debian-gcc' in the sysreqs::sysreqs() call.

I think (?) my problem is that the below three calls do not yield the same result in the above reprex:

1. Rscript -e "sysreqs::sysreqs(desc = 'DESCRIPTION', platform = 'linux-x86_64-debian-gcc')":
   does not work in above reprex: installing (e.g.) {data.table} fails with zlib.h: No such file or directory.
   ({data.table} has a SystemRequirements: zlib.)
2. sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION', platform = 'linux-x86_64-debian-gcc'))") && eval "$sysreqs":
   works
3. export DEBIAN_FRONTEND=noninteractive; apt-get -y update && apt-get install -y zlib1g-dev:
   works, because it's the same as 2.

I had assumed that 1. would also work, but there seems to be a subtle difference between 1 and 2/3, though this difference only kicks in for rocker/rstudio:3.6.2 (and presumably other debian images?) not rhub/debian-gcc-release.

[gaborcsardi]

yes, sorry, that wasn't my problem here.

Right, sorry, too quick reading. :) Yeah, sysreqs::sysreqs() just returns the canonical names of the system requirements, not the install commands.

It probably only worked on the rhub container, because that has zlib-dev already.

[maxheld83]

Yikes, I’m so dense. Sorry about that.