search

Bioconductor / bioc_docker

[DEPRECATED] Docker containers for Bioconductor
https://github.com/bioconductor/bioconductor_docker
Artistic License 2.0
49 stars 26 forks source link

Add libmariadb-dev instead of libmariadb-dev-compat #92

Closed nturaga closed 5 years ago

nturaga commented 5 years ago

For a few reasons,

1. libmariadb-dev-compat causes RStudio to fail startup,

```
[services.d] starting services
/usr/lib/rstudio-server/bin/rserver: error while loading shared libraries: libssl.so.1.0.2: cannot open shared object file: No such file or directory
[services.d] done.
rsession: no process found
```

This is because libmariadb-dev-compat introduces a new installation of libssl.so which isn't avialable on the machine (namely, libssl.so.1.0.0).

This can be verified by, starting the docker image, then within `/usr/lib/x86_64-linux-gnu`,

```
root@dfabeee53986:/usr/lib/x86_64-linux-gnu# ls libssl*
libssl.a  libssl.so  libssl.so.1.0.0  libssl.so.1.1
```

What we want from the image is to look exactly the same as from the rocker/rstudio:devel image which has,

```
root@dfabeee53986:/usr/lib/x86_64-linux-gnu# ls libssl*
libssl.a  libssl.so  libssl.so.1.1
```

2. libmariadb-dev doesn't introduce the new installation of libssl.

3. Allows RStudio startup and installation of packages like RMariaDB and GenomicFeatures without issues.

libmariadb-dev-compat doesn't cause the same issue in RELEASE_3_10 image but we are changing it anyway. RStudio works as expected with the change.