Error: Docker RStudio-server, unable to connect to service

[LeonSaal]

Hi Rick,

today I pulled the latest image version with:
docker pull uva-hva.gitlab.host:4567/r.helmus/patroon/patroonrs (sha256:1f4bea6165ff72ab7e8c6984814034ccdb7d25b98829572c7a1cc2e04ebd2946)

And ran it with:
docker run --rm -p 8787:8787 -u 0 uva-hva.gitlab.host:4567/r.helmus/patroon/patroonrs /init

However, after the login-page, a connection to R could not be established.

The logfiles state, that some library versions are unavailable.

/usr/lib/rstudio-server/bin/rsession: /lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/lib/rstudio-server/bin/rsession)
/usr/lib/rstudio-server/bin/rsession: /lib/libstdc++.so.6: version `CXXABI_1.3.13' not found (required by /usr/lib/rstudio-server/bin/rsession)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/rstudio-server/bin/rsession)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.32' not found (required by /usr/lib/rstudio-server/bin/rsession)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/rstudio-server/bin/rsession)
/usr/lib/rstudio-server/bin/rsession: /lib/libm.so.6: version `GLIBC_2.35' not found (required by /usr/local/lib/R/lib/libR.so)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/local/lib/R/lib/libR.so)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/local/lib/R/lib/libR.so)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libsqlite3.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libsqlite3.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libpq.so.5)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.32' not found (required by /usr/lib/x86_64-linux-gnu/libpq.so.5)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libcrypto.so.3)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libcrypto.so.3)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libreadline.so.8)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.32' not found (required by /usr/lib/x86_64-linux-gnu/liblzma.so.5)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/liblzma.so.5)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.32' not found (required by /usr/lib/x86_64-linux-gnu/libtirpc.so.3)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libtirpc.so.3)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libicuuc.so.70)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libicuuc.so.70)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libldap-2.5.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libldap-2.5.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libopenblas.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libtinfo.so.6)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libkrb5.so.3)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libkrb5.so.3)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libk5crypto.so.3)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libkrb5support.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libkrb5support.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libsasl2.so.2)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libgnutls.so.30)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libgnutls.so.30)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libgfortran.so.5)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libgfortran.so.5)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libresolv.so.2)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.33' not found (required by /usr/lib/x86_64-linux-gnu/libp11-kit.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libp11-kit.so.0)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.32' not found (required by /usr/lib/x86_64-linux-gnu/libunistring.so.2)
/usr/lib/rstudio-server/bin/rsession: /lib/libc.so.6: version `GLIBC_2.34' not found (required by /usr/lib/x86_64-linux-gnu/libunistring.so.2)

Is there anything I can do differently or can this problem only be fixed by a new image build?

Regards,

Leon

[rickhelmus]

Hi Leon,

Thanks for bringing this up. It seems updating the base image is enough to fix this. However, other things are failing for different reasons (XCMS, MS2Quant, TeX documentation...) It's all a bit out of my hand, but I'll see if I can find some workarounds soon.

Thanks,
Rick

[rickhelmus]

Alright, after many struggles, it turned out OpenMS 3.0 was causing these problems. But I think I found the right workarounds for that and everything seems to work fine again. I'm currently fixing a few other things for 2.3.1, but you can probably work with the latest image now.