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:
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.continuum.io/pkgs/main/linux-64
- https://repo.continuum.io/pkgs/main/noarch
- https://repo.continuum.io/pkgs/free/linux-64
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/linux-64
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/linux-64
- https://repo.continuum.io/pkgs/pro/noarch
libicui18n.so
library. Please edit your question and tell us what operating system you are using. If Linux, tell us what distribution. $\endgroup$CentOS
. I am working withrstudio
on the cluster. $\endgroup$yum search libicui18n
(if that returns nothing, tryyum search libicui
or evenyum 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). $\endgroup$No matches found
. Also, I do not haveroot
privileges obviously, so maybe I should download thislibicui18n.so
library and install it locally somehow? $\endgroup$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. $\endgroup$