stringi.so Is missing on conda enviroments

[geparada]

Hello there!

I am having some issues with stringi when I try to get it run from a conda envirioment. This is the error I am currently getting:

processing file: final_filters2.Rmd
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/lustre/scratch117/cellgen/team218/gp7/miniconda/lib/R/library/stringi/libs/stringi.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning messages:
1: In grDevices::png(tempfile()) :
  unable to load shared object '/lustre/scratch117/cellgen/team218/gp7/miniconda/lib/R/library/grDevices/libs//cairo.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
2: In grDevices::png(tempfile()) : failed to load cairo DLL
Execution halted

It seems that other people have had this issue before and it might have to do with the compiler call: https://stackoverflow.com/questions/46735932/rstudio-how-to-get-stringi-package-installation-to-work-all-good-until-dyn-load

I would be very grateful if you can give me any ideas about how to solve this, as I would like to keep using this R-script (final_filters2.Rmd) string within a conda enviroment that run though SnakeMake.

Best, Guillermo

Environment (conda list):

``` channels: - conda-forge - bioconda - biobuilds dependencies: - r-ggplot2 - r-reshape2 - r-stringr - r-mixtools - r-data.table - r-stringi - pandoc ```

Details about conda and system ( conda info ):

``` active environment : MicroExonator_R active env location : /lustre/scratch117/cellgen/team218/gp7/miniconda/envs/MicroExonator_R shell level : 2 user config file : /nfs/users/nfs_g/gp7/.condarc populated config files : /nfs/users/nfs_g/gp7/.condarc conda version : 4.6.7 conda-build version : not installed python version : 2.7.12.final.0 base environment : /lustre/scratch117/cellgen/team218/gp7/miniconda (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/cgat/linux-64 https://conda.anaconda.org/cgat/noarch package cache : /lustre/scratch117/cellgen/team218/gp7/miniconda/pkgs /nfs/users/nfs_g/gp7/.conda/pkgs envs directories : /lustre/scratch117/cellgen/team218/gp7/miniconda/envs /nfs/users/nfs_g/gp7/.conda/envs platform : linux-64 user-agent : conda/4.6.7 requests/2.21.0 CPython/2.7.12 Linux/3.2.0-105-generic ubuntu/12.04.5 glibc/2.15 UID:GID : 15375:1535 netrc file : None offline mode : False ```

[geparada]

Hello there:

I managed to make it work! Maybe I was not activating the environment correctly when I was running SnakeMake. Also, I just had to add r-rmarkdown to the environment and now is working fine. I am sorry if I miss reported this issue, but I will now close it.

[jdblischak]

I was having a similar problem. I fixed it by setting strict channel priority and re-installing to make sure all the packages were installed from conda-forge.

conda config --set channel_priority strict