Question: R packages error - unable to load shared object
1
gravatar for Francis
4 weeks ago by
Francis10
Francis10 wrote:

I use the conda update the R language and then I require packages but there is a error.

> unable to load shared object
> '/home/slee_pkuhpc/lustre1/test/software/miniconda2/lib/R/modules//internet.so':
> libssl.so.1.0.0: cannot open shared object file: No such file or
> directory

I Googled the question but I did not find a fix. I do not have the root authority and do not change something.

So any advice is helpful.

Thanks.

conda miniconda R • 154 views
ADD COMMENTlink modified 4 weeks ago by zx87546.8k • written 4 weeks ago by Francis10
1

HI Francis,

I think that the category tool is for announcing tools that you are making available, not for asking questions regarding tools (everybody is asking questions regarding a bioinformatics tool, more or less!)

Not having root permission complicates things. Looks like you have some problems with ssl libraries. Try to give a looke here: https://askubuntu.com/questions/339364/libssl-so-10-cannot-open-shared-object-file-no-such-file-or-directory. One idea could be to also include the ssl libraries in the conda environment you are building for R, but I am not very expert on this.

Another option could be to see if you manage to install R without root permission: try to see if these posts help:

https://unix.stackexchange.com/questions/149451/install-r-in-my-own-directory

https://community.rstudio.com/t/installing-other-version-of-r-without-root-access-and-working-on-rstudio-server/5275/5

ADD REPLYlink written 4 weeks ago by Fabio Marroni2.1k

Ok, Devon already solved the problem... Thanks Devon, I might need this trick!!!

ADD REPLYlink written 4 weeks ago by Fabio Marroni2.1k

This is biting everyone at the moment, unfortunately :(

ADD REPLYlink written 4 weeks ago by Devon Ryan88k

I am sorry about the category and thanks for your advice. I learn something from this links, thank you.

ADD REPLYlink written 29 days ago by Francis10
7
gravatar for Devon Ryan
4 weeks ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:
conda install openssl==1.0.2p

What you're observing happens when you use conda install inside an environment that has packages with pinned dependencies for which an updated version of the dependency is available. Since conda install seemingly ignores pinnings, it gleefully updates everything in the environment thereby randomly breaking things. The best practices are one of the following:

  • Use conda create to make a new environment for software packages/combinations
  • Use --no-update-deps so conda doesn't try to update everything if you MUST use conda install
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Devon Ryan88k

Thanks for your answer. I am sorry that the reply is late.

Yes, it`s a good ideal to creat a new environment for analysis. I uninstalled miniconda and reinstalled again, it works now.

Thanks!

ADD REPLYlink written 29 days ago by Francis10
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