bioconductor/devel_base2:latest image -- libssl1.0.2 issue

[nturaga]

docker run -p 8787:8888 -e PASSWORD=bioc bioconductor/devel_base2:latest              ✔
[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] add: executing...
Nothing additional to add
[cont-init.d] add: exited 0.
[cont-init.d] userconf: executing...
[cont-init.d] userconf: exited 0.
[cont-init.d] done.
[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

Issue carries forward to https://github.com/Bioconductor/bioconductor_full/issues/18

[nturaga]

It seems the bug is introduced by introducing the library libmariadb-dev-compat in the devel version.

This seems to be adding a version of libssl.so.1.0.0 in /usr/lib/x86_64-linux-gnu. And this is causing the problem with rstudio.

If I remove this library libmariadb-dev-compat from the Dockerfile, there are only, (rstudio works)

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

Next step is to investigate why we need libmariadb-dev-compat.

[lshep]

you originally had libmariadb-client-lgpl-dev in the dockerfile but this is what also broke in devel a few weeks ago. While you were away @mtmorgan and I chose this as the replacement. If you have a better dependency, I'm fine with changing to whatever is appropriate.

[nturaga]

Yes, that still isn't introducing a bug in debian stretch (RELEASE_3_10). I'm testing libmariadb-dev on buster to see if it fits our needs. It currently doesn't introduce the bug for Rstudio, but I need to check if Bioconductor packages which depend on it install successfully.

[nturaga]

This is now resolved. The latest release_base2 and devel_base2 images work as expected.

[drisso]

Not sure if this is the right place to put this, but I've encountered the same error running:

docker run -e PASSWORD=bioc -p 8787:8787 bioconductor/devel_core2

so perhaps the same fix should be applied to *_core2 images?

[lshep]

I've just kicked off the rebuild of devel_core it should be available shortly.

[nturaga]

The core images have to be rebuilt off the base images.

On Mon, Nov 25, 2019 at 10:28 AM Davide Risso notifications@github.com wrote:

Not sure if this is the right place to put this, but I've encountered the same error running:

docker run -e PASSWORD=bioc -p 8787:8787 bioconductor/devel_core2

so perhaps the same fix should be applied to *_core2 images?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/bioc_docker/issues/91?email_source=notifications&email_token=AAU6QS6YECRAE4ZFDXHQSODQVPVLRA5CNFSM4JPWOV5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFCY2OI#issuecomment-558206265, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAU6QS6KRXTQXBSTCDFDSJLQVPVLRANCNFSM4JPWOV5A .