Error compiling htmltools when building the image

[olea]

Hi:

When building the docker image it can't finish the htmltools instalation. Building with docker build -t metashark .

* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c template.c -o template.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o htmltools.so init.o template.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-htmltools/00new/htmltools/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
mv: cannot overwrite non-directory '/usr/local/lib/R/site-library/htmltools' with directory '/usr/local/lib/R/site-library/00LOCK-htmltools/00new/htmltools'
ERROR:   moving to final location failed
* restoring previous ‘/usr/local/lib/R/site-library/htmltools’
Error in i.p(...) : 
  (converted from warning) installation of package ‘htmltools’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
Error: error building at STEP "RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.0.0")'": error while running runtime: exit status 1

Application data:

$ git info --no-config

## Remote URLs:

origin	git@github.com:earnaud/MetaShARK_docker.git (fetch)
origin	git@github.com:earnaud/MetaShARK_docker.git (push)

## Remote Branches:

  origin/HEAD -> origin/master
  origin/master
  origin/stable

## Local Branches:

* master

## Most Recent Commit:

commit 9e3b50dcbaece50236ae9dafb580ed675576e49e
Author: Elie Ker Arno <earnaud@outlook.com>

    MetaShARK updated

No configuration changes:

$ git diff .

Using Fedora Linux 32. I'm very familiar with Linux application compiling but not with R ecosystem.

Could you please provide some advice?

[yvanlebras]

Dear olea,

Thank you for reporting your error and for trying using MetaShARK! Maybe I can give you this link https://hub.docker.com/r/eliearnaud/metashark towards the last Docker image of MetaShARK you can directly use to create a container.

Moreover, it seems to me this repo is out of date, but you can directly use the Dockerfile from the main MetaShARK code repo https://github.com/earnaud/MetaShARK-v2 .

Sorry if we forget to update this repo, and please, don't hesitate to come back to us if you have issue, comments or questions!

[olea]

Not sure if it was the same problem than earnaud/MetaShARK-v2#163, but close this anyway.