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I'm trying to install packages necessary for bioinformatics analysis on R, running on AlmaLinux. I keep getting missing dependencies messages, but when I try installing one of those dependencies, it turns out to have missing dependencies of its own.

I have an R library for my non-root user, and the R folder, including the library, is owned by this user, and I have all permissions set (rwx).

I'm currently trying to install the Seurat package using install.packages("Seurat"), and also BiocManager::install("Seurat"). Neither works, and I get the following:

Error: package or namespace load failed for ‘igraph’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/nghlm/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-igraph/00new/igraph/libs/igraph.so':
  libicui18n.so.58: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/nghlm/R/x86_64-pc-linux-gnu-library/4.2/igraph’
ERROR: dependency ‘igraph’ is not available for package ‘leiden’
* removing ‘/home/nghlm/R/x86_64-pc-linux-gnu-library/4.2/leiden’
ERROR: dependency ‘rgeos’ is not available for package ‘SeuratObject’
* removing ‘/home/nghlm/R/x86_64-pc-linux-gnu-library/4.2/SeuratObject’
ERROR: dependencies ‘igraph’, ‘leiden’, ‘SeuratObject’ are not available for package ‘Seurat’
* removing ‘/home/nghlm/R/x86_64-pc-linux-gnu-library/4.2/Seurat’

The downloaded source packages are in
    ‘/tmp/RtmpGPBmHt/downloaded_packages’
Warning messages:
1: In install.packages(...) :
  installation of package ‘rgeos’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘igraph’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘leiden’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘SeuratObject’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘Seurat’ had non-zero exit status

Here's my session info:

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: AlmaLinux 8.6 (Sky Tiger)

Matrix products: default
BLAS:   /home/nghlm/R/lib64/R/lib/libRblas.so
LAPACK: /home/nghlm/R/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.18 compiler_4.2.0      tools_4.2.0
halfer
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  • You could add some code on how you are attempting to install igraph... this can lead you to more specific answers... – hamagust Jun 02 '22 at 14:51
  • What command did you use - does this flavour of Linux use Apt or Yum? – halfer Jun 02 '22 at 17:02
  • If you are completely stuck and need to move forward, then you could install R either via Docker or Virtual Box - a bit fiddly but might get you over the line, and then you can fix the issue at your leisure in your host machine. – halfer Jun 02 '22 at 17:03
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    @hamagust Thanks. I will try the method in the link, but I'm actually trying to install the Seurat package, which seems to depend on igraph. (I will add the code now.) – Abdullah Khasawneh Jun 02 '22 at 23:39
  • @halfer Thanks. I shall try to use Docker, although I'm not sure I can handle it yet. Also, this distro uses yum and/or dnf. I have added the R commands I tried to install the packages. – Abdullah Khasawneh Jun 02 '22 at 23:44
  • The "unable to load shared object" is the problem - have a look in `/home/nghlm/R/x86_64-pc-linux-gnu-library/` to see if there are other kernel versions in there. – halfer Jun 03 '22 at 11:22
  • Thanks. Actually, it turned out to be that I was missing libssl on the OS itself, which I thought I had. Thank you for the help. Unfortunately, I can't add an answer now, since the questionhas already been closed too early. – Abdullah Khasawneh Jun 06 '22 at 02:46
  • The linked question is an exact duplicate - do please post your answer there – halfer Jun 06 '22 at 10:06
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    @halfer Thanks! I have now, and it has even taught me how to look up packages recently installed on the OS! – Abdullah Khasawneh Jun 07 '22 at 23:53

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