Unable to load immunedeconv

[malonzm1]

Hi,

When I try to load immunedeconv, I get the following error message:

library(immunedeconv)
Loading required package: EPIC
Error: package or namespace load failed for ‘immunedeconv’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/R/x86_64-pc-linux-gnu-library/4.1/Matrix/libs/Matrix.so':
/R/x86_64-pc-linux-gnu-library/4.1/Matrix/libs/Matrix.so: undefined symbol: libintl_dgettext

Please advise.

Thanks and good day.

[mlist]

Have you tried to load the package in a clean R session?

[malonzm1]

Thanks. I'm not sure what a clean R session is but library(immunedeconv) was the first command I entered.

[mlist]

In Rstudio this would be session - restart R session.

[malonzm1]

I think it was a clean session since I just opened R in the terminal when I entered the command.

[mlist]

How did you install immunedeconv? We highly recommend using conda for installation as this leads to a standardized environment which works out more often than the R package installation where sometimes missing system packages or R package incompatibilities cause problems.

[malonzm1]

I installed it with conda install -c bioconda -c conda-forge r-immunedeconv as shown in https://omnideconv.org/immunedeconv/.

[mlist]

just to be sure, did you activate the environment prior to loading the package?

[malonzm1]

Yes.

[alex-d13]

Hi,

it looks like the Matrix package might not have been installed correctly. Could you try to re-install it with install.packages("Matrix")?
(Similar to this issue: https://stackoverflow.com/questions/38943764/r-error-in-dyn-loadfile-dllpath-dllpath)

[malonzm1]

The new error is the following:

library(immunedeconv)
Loading required package: EPIC
Error: package or namespace load failed for ‘immunedeconv’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/R/x86_64-pc-linux-gnu-library/4.1/stringi/libs/stringi.so':
libicui18n.so.67: cannot open shared object file: No such file or directory

[alex-d13]

Ok, so a different package is also not installed correctly (stringi).

I am not sure this is a immunedeconv issue, it seems like there might have been some things that went wrong during the installation of packages that immunedeconv depends on.

[LorenzoMerotto]

In this case I would try to install immunedeconv in a normal R session, without using conda, and see if the problem persists