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When I am trying to install Seurat in R markdown file:

install.packages("Seurat")

it fails with the following errors:

Installing package into ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)
Warning in install.packages :
  dependency ‘proxy’ is not available
also installing the dependencies ‘igraph’, ‘dtw’, ‘diffusionMap’

trying URL 'https://cran.rstudio.com/src/contrib/igraph_1.2.1.tar.gz'

Content type 'unknown' length 2703426 bytes (2.6 MB)

downloaded 2.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/dtw_1.18-1.tar.gz'

Content type 'unknown' length 849256 bytes (829 KB) downloaded 829 KB trying URL 'https://cran.rstudio.com/src/contrib/diffusionMap_1.1-0.tar.gz'

Content type 'unknown' length 39130 bytes (38 KB)
downloaded 38 KB

trying URL 'https://cran.rstudio.com/src/contrib/Seurat_2.3.0.tar.gz'

Content type 'unknown' length 846065 bytes (826 KB)

downloaded 826 KB
* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
installing to /sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

Error in dyn.load(file, DLLpath = DLLpath, ...) :    unable to load shared object '/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/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 ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/igraph’ Warning in install.packages :   installation of package ‘igraph’ had non-zero exit status

ERROR: dependency ‘proxy’ is not available for package ‘dtw’
* removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/dtw’ Warning in install.packages :   installation of package ‘dtw’ had non-zero exit status

ERROR: dependency ‘igraph’ is not available for package ‘diffusionMap’
* removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/diffusionMap’ Warning in install.packages :   installation of package ‘diffusionMap’ had non-zero exit status

ERROR: dependencies ‘igraph’, ‘dtw’, ‘diffusionMap’ are not available for package ‘Seurat’
* removing ‘/sfs/qumulo/qhome/nv4e/R/x86_64-pc-linux-gnu-library/3.3/Seurat’ Warning in install.packages :   installation of package ‘Seurat’ had non-zero exit status

How could it be fixed? What to try?

Operating system is CentOS Linux release 7.3.1611 (Core)

Update

I also tried development version of Seurat but it failed too: http://satijalab.org/seurat/devinstall.html

Update

I tried installing Seurat using conda install -c bioconda r-seurat and it is not working. It is giving the error:

-bash-4.2$ conda install -c bioconda r-seurat Fetching package metadata ............. Solving package specifications:

PackageNotFoundError: Packages missing in current channels:

  • r-seurat -> r-cowplot
  • r-seurat -> r-diffusionmap
  • r-seurat -> r-dtw
  • r-seurat -> r-ggridges
  • r-seurat -> r-ica
  • r-seurat -> r-pbapply
  • r-seurat -> r-ranger
  • r-seurat -> r-rcppprogress
  • r-seurat -> r-sdmtools
  • r-seurat -> r-tclust

We have searched for the packages in the following channels:

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  • $\begingroup$ You seem to be missing the libicui18n.so library. Please edit your question and tell us what operating system you are using. If Linux, tell us what distribution. $\endgroup$
    – terdon ♦
    Apr 25, 2018 at 18:26
  • $\begingroup$ I just updated. It is CentOS. I am working with rstudio on the cluster. $\endgroup$
    – Nikita Vlasenko
    Apr 25, 2018 at 18:49
  • $\begingroup$ Ah, thanks. So what is the output of yum search libicui18n (if that returns nothing, try yum search libicui or even yum search icui until you get a result). Then, install the package. If that works, let me know and I can post answer (or just post it yourself, up to you). $\endgroup$
    – terdon ♦
    Apr 25, 2018 at 18:57
  • $\begingroup$ The output in all the three cases is No matches found. Also, I do not have root privileges obviously, so maybe I should download this libicui18n.so library and install it locally somehow? $\endgroup$
    – Nikita Vlasenko
    Apr 25, 2018 at 19:40
  • $\begingroup$ Hmm, I haven't used an rpm-based system in ages. You might need to search for libicui* or something. I did check CentOS's repository, and there is such a package. I don't remember how to install rpms locally though and I'm on mobile, so I can't help much. You could try asking how to find and install the relevant package on Unix & Linux. $\endgroup$
    – terdon ♦
    Apr 25, 2018 at 19:56

1 Answer 1

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As @terdon mentioned in the comments, you need to sudo yum install libicu on the relevant nodes (or have your admin do that for you). Alternatively, seurat can be installed via conda, which means you don't need root access.

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  • $\begingroup$ Actually I tried installing Seurat using conda install -c bioconda r-seurat and it is not working. It is giving PackageNotFoundError. $\endgroup$
    – Nikita Vlasenko
    Apr 25, 2018 at 22:15
  • $\begingroup$ You need -c conda-forge too. You might then need to fix readline with conda upgrade -c conda-forge readline. $\endgroup$
    – Devon Ryan
    Apr 26, 2018 at 6:50
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    $\begingroup$ If you don't wish to use conda as your r package manager (because, for a start, it will install a new copy of R with its own library), you can install just ICU with conda conda install -c conda-forge icu, and then install seurat in R $\endgroup$
    – Ian Sudbery
    Apr 26, 2018 at 8:25

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